Variant report

Variant	rs57625476
Chromosome Location	chr3:142392019-142392020
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	chr3:142391997-142392019	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
RN7SKP25	TF binding region

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1479135	1.00[EUR][1000 genomes]
rs1479138	1.00[EUR][1000 genomes]
rs2199714	1.00[EUR][1000 genomes]
rs34502778	1.00[EUR][1000 genomes]
rs35582603	1.00[EUR][1000 genomes]
rs35978765	1.00[EUR][1000 genomes]
rs3924057	1.00[EUR][1000 genomes]
rs55820583	1.00[EUR][1000 genomes]
rs55895932	1.00[EUR][1000 genomes]
rs56022646	1.00[EUR][1000 genomes]
rs56050554	1.00[EUR][1000 genomes]
rs56062708	1.00[EUR][1000 genomes]
rs56921402	1.00[EUR][1000 genomes]
rs58421597	1.00[EUR][1000 genomes]
rs58980616	1.00[EUR][1000 genomes]
rs59181450	0.89[AFR][1000 genomes]
rs59456283	1.00[EUR][1000 genomes]
rs59936227	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60399161	1.00[EUR][1000 genomes]
rs60403314	1.00[EUR][1000 genomes]
rs60701561	1.00[EUR][1000 genomes]
rs61244634	1.00[EUR][1000 genomes]
rs61300208	1.00[EUR][1000 genomes]
rs61326325	1.00[EUR][1000 genomes]
rs6440101	1.00[EUR][1000 genomes]
rs6765644	1.00[EUR][1000 genomes]
rs6768384	1.00[EUR][1000 genomes]
rs6770411	1.00[EUR][1000 genomes]
rs6776083	1.00[EUR][1000 genomes]
rs6777735	1.00[EUR][1000 genomes]
rs6781412	1.00[EUR][1000 genomes]
rs6791858	1.00[EUR][1000 genomes]
rs6792428	1.00[EUR][1000 genomes]
rs6798670	1.00[EUR][1000 genomes]
rs72988608	1.00[EUR][1000 genomes]
rs72988609	1.00[EUR][1000 genomes]
rs72988618	1.00[EUR][1000 genomes]
rs72988639	1.00[EUR][1000 genomes]
rs72990712	1.00[EUR][1000 genomes]
rs72990731	1.00[EUR][1000 genomes]
rs72990738	1.00[EUR][1000 genomes]
rs72990743	1.00[EUR][1000 genomes]
rs72992635	1.00[EUR][1000 genomes]
rs72992638	1.00[EUR][1000 genomes]
rs72992653	1.00[EUR][1000 genomes]
rs73002081	1.00[EUR][1000 genomes]
rs73002088	1.00[EUR][1000 genomes]
rs73002089	1.00[EUR][1000 genomes]
rs73002093	1.00[EUR][1000 genomes]
rs73003968	1.00[EUR][1000 genomes]
rs73003973	1.00[EUR][1000 genomes]
rs73864409	1.00[EUR][1000 genomes]
rs73864413	1.00[EUR][1000 genomes]
rs73864431	1.00[EUR][1000 genomes]
rs7613884	1.00[EUR][1000 genomes]
rs7615480	1.00[EUR][1000 genomes]
rs7620068	1.00[EUR][1000 genomes]
rs7620319	1.00[EUR][1000 genomes]
rs7621810	1.00[EUR][1000 genomes]
rs7622266	1.00[EUR][1000 genomes]
rs7625306	1.00[EUR][1000 genomes]
rs7625764	1.00[EUR][1000 genomes]
rs7628677	1.00[EUR][1000 genomes]
rs7630817	1.00[EUR][1000 genomes]
rs7648475	1.00[EUR][1000 genomes]
rs7652760	1.00[EUR][1000 genomes]
rs7653387	1.00[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932989	chr3:142204208-142423305	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142366000-142435400	Weak transcription	Colonic Mucosa	Colon
2	chr3:142369400-142408400	Weak transcription	Pancreas	Pancrea
3	chr3:142371000-142393800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:142379200-142413000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:142382600-142400400	Weak transcription	Gastric	stomach
6	chr3:142384400-142411400	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr3:142384600-142392400	Weak transcription	HepG2	liver
8	chr3:142384800-142403000	Weak transcription	Liver	Liver
9	chr3:142385800-142415400	Weak transcription	A549	lung
10	chr3:142386400-142411800	Weak transcription	NHEK	skin
11	chr3:142387400-142401800	Weak transcription	Aorta	Aorta
12	chr3:142387400-142404200	Weak transcription	Small Intestine	intestine
13	chr3:142387400-142413400	Weak transcription	Stomach Mucosa	stomach
14	chr3:142388200-142393200	Strong transcription	Duodenum Mucosa	Duodenum
15	chr3:142388200-142393200	Strong transcription	Rectal Mucosa Donor 31	rectum
16	chr3:142389200-142412400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr3:142389200-142414800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr3:142389400-142408800	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr3:142389400-142410000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr3:142389800-142442400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr3:142390000-142392800	Strong transcription	Dnd41	blood
22	chr3:142390000-142406200	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr3:142390400-142393000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr3:142391000-142392600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr3:142391200-142394800	Strong transcription	Fetal Intestine Small	intestine
26	chr3:142391200-142395400	Weak transcription	Lung	lung
27	chr3:142391600-142393000	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr3:142391800-142392400	Strong transcription	Fetal Intestine Large	intestine
29	chr3:142391800-142393000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr3:142391800-142393400	Strong transcription	Primary hematopoietic stem cells	blood
31	chr3:142392000-142392800	Strong transcription	Sigmoid Colon	Sigmoid Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links