Variant report

Variant	rs12032801
Chromosome Location	chr1:47900527-47900528
allele	A/C
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	POLR2A	chr1:47899546-47900621	H1-neurons	neurons:	n/a	n/a
2	SUZ12	chr1:47898147-47900955	H1-hESC	embryonic stem cell:	n/a	n/a
3	CTBP2	chr1:47899428-47900976	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
FOXD2-AS1	TF binding region
FOXD2	TF binding region

Extended variants
information (count: 42 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11211529	1.00[EUR][1000 genomes]
rs11211536	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12021515	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12026379	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12030146	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12049163	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12049416	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1680019	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17103177	1.00[EUR][1000 genomes]
rs17103179	1.00[EUR][1000 genomes]
rs17103196	1.00[EUR][1000 genomes]
rs1765156	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1813427	1.00[EUR][1000 genomes]
rs2253511	1.00[EUR][1000 genomes]
rs2506984	1.00[EUR][1000 genomes]
rs2622906	1.00[EUR][1000 genomes]
rs2622911	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs3738317	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4926868	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs495482	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs506329	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs522768	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs527430	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs557101	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59366267	0.81[ASN][1000 genomes]
rs60042036	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61784813	0.82[ASN][1000 genomes]
rs642750	1.00[EUR][1000 genomes]
rs6683513	0.87[EUR][1000 genomes]
rs6688278	0.87[EUR][1000 genomes]
rs66904716	1.00[EUR][1000 genomes]
rs6703935	1.00[EUR][1000 genomes]
rs693036	1.00[EUR][1000 genomes]
rs72480616	1.00[EUR][1000 genomes]
rs72553947	1.00[EUR][1000 genomes]
rs72553949	1.00[EUR][1000 genomes]
rs72637985	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv871961	chr1:47875627-47912628	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv534956	chr1:47882277-47905486	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv534957	chr1:47882277-47907965	Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1001779	chr1:47884229-48111485	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv871299	chr1:47889417-48057890	Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47894400-47901600	Weak transcription	HepG2	liver
2	chr1:47896800-47900600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
3	chr1:47897000-47901600	Weak transcription	A549	lung
4	chr1:47897200-47900600	Bivalent Enhancer	Fetal Stomach	stomach
5	chr1:47898000-47900600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr1:47898200-47901000	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:47898400-47900800	Bivalent Enhancer	Esophagus	oesophagus
8	chr1:47898600-47900600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
9	chr1:47898600-47900600	Bivalent Enhancer	Fetal Brain Male	brain
10	chr1:47898600-47900800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr1:47898600-47900800	Bivalent Enhancer	Placenta	Placenta
12	chr1:47898600-47901200	Weak transcription	Hela-S3	cervix
13	chr1:47898800-47900600	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
14	chr1:47898800-47901400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr1:47898800-47901600	Weak transcription	K562	blood
16	chr1:47898800-47902000	Weak transcription	HSMM	muscle
17	chr1:47898800-47902000	Weak transcription	HSMMtube	muscle
18	chr1:47899000-47901200	Genic enhancers	Dnd41	blood
19	chr1:47899000-47901400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr1:47899000-47904400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
21	chr1:47899200-47900600	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
22	chr1:47899200-47901800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr1:47899200-47902200	Weak transcription	Gastric	stomach
24	chr1:47899400-47900600	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
25	chr1:47899400-47900600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr1:47899400-47900600	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
27	chr1:47899400-47900600	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
28	chr1:47899400-47901600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr1:47899400-47901600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr1:47899800-47900800	Bivalent Enhancer	Brain Angular Gyrus	brain
31	chr1:47899800-47901000	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
32	chr1:47899800-47901800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr1:47900000-47900600	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
34	chr1:47900000-47900600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
35	chr1:47900000-47900600	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
36	chr1:47900000-47900800	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
37	chr1:47900000-47902000	Enhancers	Aorta	Aorta
38	chr1:47900200-47900600	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
39	chr1:47900200-47900600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr1:47900200-47900600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr1:47900200-47900600	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
42	chr1:47900200-47900600	Bivalent Enhancer	Brain Substantia Nigra	brain
43	chr1:47900200-47900600	Bivalent Enhancer	Colon Smooth Muscle	Colon
44	chr1:47900200-47900600	Bivalent Enhancer	Stomach Mucosa	stomach
45	chr1:47900200-47900800	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr1:47900200-47900800	Bivalent Enhancer	Brain Germinal Matrix	brain
47	chr1:47900200-47900800	Bivalent/Poised TSS	Fetal Intestine Small	intestine
48	chr1:47900200-47900800	Bivalent Enhancer	Fetal Lung	lung
49	chr1:47900200-47900800	Bivalent Enhancer	HUVEC	blood vessel
50	chr1:47900200-47900800	Enhancers	NHLF	lung

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