Variant report

Variant	rs72997586
Chromosome Location	chr1:146713635-146713636
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr1:146713572-146713891	MCF10A-Er-Src	breast:	n/a	chr1:146713719-146713731 chr1:146713721-146713729 chr1:146713720-146713730
2	GATA1	chr1:146713626-146714801	PBDE	blood:	n/a	n/a
3	MAFF	chr1:146713579-146714169	K562	blood:	n/a	n/a
4	HCFC1	chr1:146713350-146715947	Hela-S3	cervix:	n/a	n/a
5	CTCF	chr1:146713528-146715647	SK-N-SH	brain:	n/a	chr1:146714231-146714244 chr1:146714770-146714778 chr1:146714765-146714778 chr1:146714231-146714244 chr1:146714763-146714781 chr1:146714758-146714779 chr1:146714764-146714780 chr1:146714230-146714246 chr1:146713904-146713911 chr1:146714229-146714247
6	RCOR1	chr1:146713521-146715468	IMR90	lung:	n/a	n/a
7	HDAC2	chr1:146713602-146715538	MCF-7	breast:	n/a	n/a
8	GATA3	chr1:146713450-146714084	SH-SY5Y	brain:	n/a	n/a
9	FOS	chr1:146713614-146713781	MCF10A-Er-Src	breast:	n/a	chr1:146713719-146713731 chr1:146713721-146713729 chr1:146713720-146713730
10	MAFK	chr1:146713616-146714330	K562	blood:	n/a	chr1:146713719-146713728 chr1:146713719-146713729
11	KAP1	chr1:146713609-146714287	K562	blood:	n/a	n/a
12	SIN3AK20	chr1:146713547-146715637	MCF-7	breast:	n/a	n/a
13	RAD21	chr1:146713585-146714553	SK-N-SH	brain:	n/a	n/a
14	MAX	chr1:146713610-146715452	MCF-7	breast:	n/a	n/a
15	CTCF	chr1:146713382-146715480	A549	lung:	n/a	chr1:146714231-146714244 chr1:146714770-146714778 chr1:146714765-146714778 chr1:146714231-146714244 chr1:146714763-146714781 chr1:146714758-146714779 chr1:146714764-146714780 chr1:146714230-146714246 chr1:146713904-146713911 chr1:146714229-146714247
16	GATA3	chr1:146713450-146715328	MCF-7	breast:	n/a	chr1:146715044-146715053
17	GATA3	chr1:146713573-146714622	MCF-7	breast:	n/a	n/a
18	NR2F2	chr1:146713526-146715343	MCF-7	breast:	n/a	n/a
19	MXI1	chr1:146713417-146716045	SK-N-SH	brain:	n/a	n/a
20	MAZ	chr1:146713404-146714869	HepG2	liver:	n/a	n/a
21	POLR2A	chr1:146713635-146714508	HepG2	liver:	n/a	n/a
22	SMC3	chr1:146713529-146715418	SK-N-SH	brain:	n/a	chr1:146714765-146714779 chr1:146714231-146714245 chr1:146714765-146714775
23	MYC	chr1:146713551-146715166	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:146637222..146651713-chr1:146712141..146718911,44	MCF-7	breast:
2	chr1:146712756..146714985-chr9:19378272..19380601,2	MCF-7	breast:
3	chr1:146632272..146634531-chr1:146713179..146715784,3	MCF-7	breast:
4	chr1:146649315..146651856-chr1:146712649..146716301,4	MCF-7	breast:
5	chr1:146629607..146632064-chr1:146712714..146714253,2	MCF-7	breast:
6	chr1:146554717..146557790-chr1:146713275..146715735,7	MCF-7	breast:
7	chr1:146550590..146559110-chr1:146711930..146718078,31	K562	blood:
8	chr1:146638562..146647588-chr1:146711453..146720391,22	K562	blood:
9	chr1:146552515..146557737-chr1:146711619..146718083,31	K562	blood:
10	chr1:146640645..146647502-chr1:146711418..146719354,29	K562	blood:
11	chr1:146643464..146645140-chr1:146713602..146715704,127	MCF-7	breast:
12	chr1:146642817..146644911-chr1:146712966..146715242,14	K562	blood:
13	chr1:146696837..146698411-chr1:146712690..146714325,2	K562	blood:
14	chr1:146643493..146644893-chr1:146713471..146715076,53	MCF-7	breast:
15	chr1:146638044..146647556-chr1:146707628..146717159,48	MCF-7	breast:

Variant related genes	Relation type
CHD1L	TF binding region
ENSG00000271721	Chromatin interaction
ENSG00000201142	Chromatin interaction
ENSG00000131781	Chromatin interaction
ENSG00000273071	Chromatin interaction
ENSG00000137154	Chromatin interaction
ENSG00000237188	Chromatin interaction
ENSG00000180867	Chromatin interaction
ENSG00000131791	Chromatin interaction
ENSG00000230832	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs28745890	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58276129	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58820837	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59402704	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59689147	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60063927	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60107727	0.85[AFR][1000 genomes]
rs60565795	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6672821	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6702705	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72995589	1.00[AMR][1000 genomes]
rs72995597	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72997505	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72997514	1.00[AMR][1000 genomes]
rs72997527	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72997542	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72997571	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72997577	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72997588	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72997590	0.87[AFR][1000 genomes]
rs72999623	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72999628	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72999632	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72999634	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72999637	1.00[AMR][1000 genomes]
rs72999638	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72999639	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72999640	1.00[AMR][1000 genomes]
rs72999646	1.00[AMR][1000 genomes]
rs72999648	1.00[AMR][1000 genomes]
rs72999655	1.00[AMR][1000 genomes]
rs72999656	1.00[AMR][1000 genomes]
rs7526114	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7527846	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7535451	1.00[AMR][1000 genomes]
rs7536442	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7546133	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:28 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv872251	chr1:146152553-146803630	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
2	nsv872252	chr1:146471863-147398135	Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	112 gene(s)	inside rSNPs	diseases
3	nsv999546	chr1:146507577-147356574	Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
4	nsv535123	chr1:146507577-147356574	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
5	nsv492188	chr1:146507649-147381479	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
6	nsv916754	chr1:146507711-147417736	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	113 gene(s)	inside rSNPs	diseases
7	nsv547673	chr1:146510112-147398135	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
8	nsv547674	chr1:146522722-147396797	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
9	nsv998341	chr1:146531446-147384720	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
10	nsv535124	chr1:146531446-147384720	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
11	nsv1003493	chr1:146531446-147389944	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
12	nsv998209	chr1:146543722-147384720	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
13	nsv535126	chr1:146543722-147384720	Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
14	nsv872255	chr1:146550780-146969712	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
15	nsv872256	chr1:146556596-147410973	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
16	nsv1012331	chr1:146603479-147384720	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
17	nsv535131	chr1:146603479-147384720	Genic enhancers Strong transcription Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
18	nsv1009943	chr1:146618929-146893851	Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
19	nsv535132	chr1:146618929-146893851	Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
20	nsv872257	chr1:146643555-146724923	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
21	nsv437047	chr1:146643555-146841602	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
22	nsv1005809	chr1:146647822-146886419	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
23	nsv535134	chr1:146647822-146886419	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
24	nsv1004849	chr1:146661516-147286826	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
25	nsv535135	chr1:146661516-147286826	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
26	nsv547676	chr1:146686228-146996047	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
27	nsv872259	chr1:146688941-146724923	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
28	esv3325681	chr1:146713353-146715901	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:146709200-146713800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:146709200-146714200	Weak transcription	Gastric	stomach
3	chr1:146709400-146713800	Weak transcription	Colonic Mucosa	Colon
4	chr1:146709400-146713800	Weak transcription	Placenta	Placenta
5	chr1:146709400-146714000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr1:146709400-146714000	Weak transcription	Esophagus	oesophagus
7	chr1:146709400-146714200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr1:146710200-146713800	Enhancers	Rectal Mucosa Donor 31	rectum
9	chr1:146711200-146713800	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr1:146711600-146713800	Weak transcription	Fetal Lung	lung
11	chr1:146712000-146713800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr1:146712600-146713800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr1:146712600-146714000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr1:146712600-146714000	Weak transcription	Pancreas	Pancrea
15	chr1:146712600-146714200	Weak transcription	Lung	lung
16	chr1:146713000-146713800	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr1:146713200-146713800	Enhancers	Pancreatic Islets	Pancreatic Islet
18	chr1:146713200-146714200	Flanking Active TSS	Liver	Liver
19	chr1:146713400-146713800	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
20	chr1:146713400-146713800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr1:146713400-146713800	Enhancers	Brain Substantia Nigra	brain
22	chr1:146713400-146713800	Enhancers	Duodenum Mucosa	Duodenum
23	chr1:146713400-146713800	Enhancers	Fetal Intestine Large	intestine
24	chr1:146713400-146713800	Enhancers	Fetal Intestine Small	intestine
25	chr1:146713400-146713800	Enhancers	Stomach Mucosa	stomach
26	chr1:146713400-146713800	Enhancers	GM12878-XiMat	blood
27	chr1:146713400-146713800	Active TSS	K562	blood
28	chr1:146713400-146714000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
29	chr1:146713400-146714200	Flanking Active TSS	Dnd41	blood
30	chr1:146713400-146714200	Flanking Active TSS	HepG2	liver
31	chr1:146713600-146713800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:146713600-146713800	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
33	chr1:146713600-146713800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr1:146713600-146713800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr1:146713600-146713800	Enhancers	Primary monocytes fromperipheralblood	blood
36	chr1:146713600-146713800	Enhancers	Primary neutrophils fromperipheralblood	blood
37	chr1:146713600-146713800	Enhancers	Primary B cells from peripheral blood	blood
38	chr1:146713600-146713800	Enhancers	Primary hematopoietic stem cells	blood
39	chr1:146713600-146713800	Enhancers	Primary T helper naive cells from peripheral blood	blood
40	chr1:146713600-146713800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
41	chr1:146713600-146713800	Enhancers	Primary T helper cells PMA-I stimulated	--
42	chr1:146713600-146713800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
43	chr1:146713600-146713800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr1:146713600-146713800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr1:146713600-146713800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr1:146713600-146713800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr1:146713600-146713800	Enhancers	Adipose Nuclei	Adipose
48	chr1:146713600-146713800	Enhancers	Brain Anterior Caudate	brain
49	chr1:146713600-146713800	Enhancers	Brain Cingulate Gyrus	brain
50	chr1:146713600-146713800	Enhancers	Brain Inferior Temporal Lobe	brain

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