Variant report

Variant	rs12328100
Chromosome Location	chr2:86307128-86307129
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:86305825..86307788-chr2:86328506..86330182,2	K562	blood:
2	chr2:85956198..85956852-chr2:86306801..86307694,2	MCF-7	breast:
3	chr2:86306434..86308864-chr2:86335264..86337422,3	K562	blood:
4	chr2:86114923..86115607-chr2:86306745..86307338,2	MCF-7	breast:
5	chr2:86065067..86065898-chr2:86306625..86307152,2	K562	blood:
6	chr2:86054186..86055161-chr2:86306747..86308111,10	MCF-7	breast:
7	chr2:86115558..86116527-chr2:86306739..86307593,3	MCF-7	breast:
8	chr2:86301883..86303571-chr2:86305517..86307251,2	K562	blood:
9	chr2:86054177..86056826-chr2:86305154..86307872,2	MCF-7	breast:
10	chr2:86252057..86252850-chr2:86306651..86307239,2	MCF-7	breast:
11	chr2:86278837..86281699-chr2:86305012..86307406,2	K562	blood:
12	chr2:86054263..86055159-chr2:86306734..86307688,8	K562	blood:

No data

Variant related genes	Relation type
ENSG00000115525	Chromatin interaction
ENSG00000132300	Chromatin interaction
ENSG00000232504	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10175330	0.93[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs10184246	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10187150	0.93[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10195199	1.00[YRI][hapmap]
rs10200018	0.82[EUR][1000 genomes]
rs10202995	0.82[EUR][1000 genomes]
rs10496318	0.93[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1057893	0.93[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs1124686	0.85[AMR][1000 genomes]
rs11395	1.00[ASW][hapmap];0.84[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11885380	0.93[JPT][hapmap]
rs11899254	0.93[JPT][hapmap]
rs12465983	0.82[EUR][1000 genomes]
rs12469363	0.81[EUR][1000 genomes]
rs12469762	0.82[ASW][hapmap];0.93[JPT][hapmap]
rs12475079	0.93[JPT][hapmap]
rs12475126	0.93[JPT][hapmap]
rs12477274	1.00[ASW][hapmap];0.82[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12478097	0.93[JPT][hapmap];0.81[EUR][1000 genomes]
rs12478369	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12714167	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12714170	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12714171	0.93[JPT][hapmap];0.81[EUR][1000 genomes]
rs12714172	0.93[JPT][hapmap]
rs12714177	0.85[TSI][hapmap]
rs12714178	1.00[YRI][hapmap]
rs12996308	0.93[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs12998164	0.81[EUR][1000 genomes]
rs12999029	0.81[MKK][hapmap]
rs13007807	1.00[YRI][hapmap]
rs13013916	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13018652	0.83[EUR][1000 genomes]
rs13019073	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13024884	0.80[EUR][1000 genomes]
rs13028023	0.90[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1424522	0.93[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17027013	0.93[JPT][hapmap]
rs2241438	0.93[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2278083	0.93[JPT][hapmap];0.81[EUR][1000 genomes]
rs2278536	1.00[ASW][hapmap]
rs2288113	0.93[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs2288114	0.82[EUR][1000 genomes]
rs2288115	0.93[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2367203	0.93[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs2367204	0.93[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34263823	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3770060	0.81[EUR][1000 genomes]
rs3770061	0.81[EUR][1000 genomes]
rs3770062	0.93[JPT][hapmap];0.81[EUR][1000 genomes]
rs3770065	0.93[JPT][hapmap]
rs3770067	0.93[JPT][hapmap];0.81[EUR][1000 genomes]
rs4374375	0.93[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs4402761	0.93[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs4422155	0.93[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs4450596	0.93[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs4544439	0.93[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs62150072	0.82[EUR][1000 genomes]
rs62150074	0.81[EUR][1000 genomes]
rs6547660	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6547661	0.93[JPT][hapmap];0.81[EUR][1000 genomes]
rs6547662	0.81[EUR][1000 genomes]
rs6547663	0.81[EUR][1000 genomes]
rs6547665	0.85[TSI][hapmap]
rs6707029	1.00[CHB][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes]
rs6725372	0.93[JPT][hapmap];0.81[EUR][1000 genomes]
rs6729732	0.93[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs6731535	0.83[EUR][1000 genomes]
rs6731995	0.93[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs6735014	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs6737950	0.93[JPT][hapmap]
rs6740044	0.84[ASW][hapmap]
rs6749090	1.00[MEX][hapmap]
rs6757387	0.93[JPT][hapmap];0.81[EUR][1000 genomes]
rs715334	0.84[GIH][hapmap];0.93[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7422930	0.85[TSI][hapmap]
rs7561589	0.82[EUR][1000 genomes]
rs7566721	0.93[JPT][hapmap];0.81[EUR][1000 genomes]
rs7569853	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7572386	1.00[YRI][hapmap]
rs7608547	0.84[EUR][1000 genomes]
rs7609008	0.93[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs8244	0.93[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs876242	0.93[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9309632	0.93[JPT][hapmap]
rs9309633	0.82[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap]
rs9653508	1.00[MEX][hapmap]
rs9653569	0.93[JPT][hapmap]
rs9917140	0.81[EUR][1000 genomes]
rs9973320	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2751903	chr2:86253542-86505453	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv531380	chr2:86253552-86469217	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv870120	chr2:86265437-86343058	Strong transcription Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
4	nsv1007474	chr2:86281967-86505453	Enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv997563	chr2:86281967-86506132	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS 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 miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
6	nsv1008924	chr2:86282722-86499402	Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
7	nsv999956	chr2:86285944-86505453	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
8	nsv1012768	chr2:86285944-86506132	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
9	nsv1003207	chr2:86286314-86496732	Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
10	nsv1000441	chr2:86286314-86508168	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
11	nsv535808	chr2:86286314-86508168	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
12	nsv1004442	chr2:86286480-86506132	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
13	nsv916616	chr2:86289130-86509326	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
14	nsv458563	chr2:86292341-86507688	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
15	nsv582370	chr2:86292341-86507688	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
16	nsv1009140	chr2:86294939-86506132	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
17	nsv582371	chr2:86296566-86507688	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
18	nsv531381	chr2:86301091-86478346	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
19	nsv1001157	chr2:86301440-86508168	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs12328100	IMMT	cis	Esophagus Muscularis	GTEx
rs12328100	IMMT	cis	Artery Aorta	GTEx
rs12328100	IMMT	cis	parietal	SCAN
rs12328100	IMMT	cis	cerebellum	SCAN
rs12328100	C2orf23	cis	multi-tissue	Pritchard
rs12328100	IMMT	Cis_1M	lymphoblastoid	RTeQTL
rs12328100	POLR1A	cis	parietal	SCAN
rs12328100	MRPL35	cis	parietal	SCAN
rs12328100	MRPL35	cis	cerebellum	SCAN
rs12328100	IMMT	cis	lymphoblastoid	seeQTL
rs12328100	IMMT	cis	lung	GTEx
rs12328100	MRPL35	Cis_1M	lymphoblastoid	RTeQTL
rs12328100	MRPL35	cis	uninvolved skin	skin_eQTL
rs12328100	IMMT	cis	Whole Blood	GTEx
rs12328100	REEP1	cis	parietal	SCAN
rs12328100	IMMT	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86252000-86331200	Strong transcription	HUES64 Cell Line	embryonic stem cell
2	chr2:86264000-86332000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr2:86265200-86330000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr2:86286000-86331000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
5	chr2:86286000-86331200	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr2:86286200-86310400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
7	chr2:86286200-86311200	Strong transcription	HUES6 Cell Line	embryonic stem cell
8	chr2:86289800-86307200	Strong transcription	HepG2	liver
9	chr2:86290200-86310800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr2:86290800-86310200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr2:86290800-86314600	Strong transcription	HMEC	breast
12	chr2:86290800-86318600	Strong transcription	K562	blood
13	chr2:86290800-86322600	Strong transcription	H1 Cell Line	embryonic stem cell
14	chr2:86291000-86311200	Strong transcription	Fetal Brain Female	brain
15	chr2:86291600-86319000	Strong transcription	Cortex derived primary cultured neurospheres	brain
16	chr2:86291800-86311400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:86291800-86318800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr2:86292800-86331000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr2:86294800-86309600	Strong transcription	H9 Cell Line	embryonic stem cell
20	chr2:86295200-86323200	Strong transcription	Fetal Stomach	stomach
21	chr2:86295800-86308400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
22	chr2:86295800-86308600	Strong transcription	Brain Germinal Matrix	brain
23	chr2:86295800-86308600	Strong transcription	NHEK	skin
24	chr2:86296000-86322400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr2:86296400-86307600	Weak transcription	Fetal Heart	heart
26	chr2:86296600-86307200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr2:86297400-86307400	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr2:86298600-86307400	Weak transcription	Fetal Brain Male	brain
29	chr2:86299200-86310400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr2:86299400-86308000	Genic enhancers	Fetal Thymus	thymus
31	chr2:86299400-86308200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr2:86299800-86308000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr2:86300000-86318200	Strong transcription	Placenta	Placenta
34	chr2:86300000-86323000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr2:86300000-86331800	Weak transcription	Stomach Mucosa	stomach
36	chr2:86300400-86307800	Weak transcription	Right Atrium	heart
37	chr2:86300400-86308600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr2:86300600-86307600	Strong transcription	Muscle Satellite Cultured Cells	--
39	chr2:86300600-86307600	Strong transcription	HSMM	muscle
40	chr2:86300600-86308200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr2:86300600-86308200	Strong transcription	Rectal Smooth Muscle	rectum
42	chr2:86300800-86307200	Strong transcription	Right Ventricle	heart
43	chr2:86300800-86307600	Strong transcription	NHDF-Ad	bronchial
44	chr2:86300800-86309000	Strong transcription	Osteobl	bone
45	chr2:86300800-86310200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr2:86301200-86307200	Weak transcription	Fetal Kidney	kidney
47	chr2:86301200-86318200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr2:86301400-86307800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr2:86302800-86307800	Weak transcription	Small Intestine	intestine
50	chr2:86303400-86310400	Strong transcription	Left Ventricle	heart

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