Variant report

Variant	rs7313825
Chromosome Location	chr12:12607856-12607857
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	EP300	chr12:12606525-12608066	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
ENSG00000271370	TF binding region

Extended variants
information (count: 76 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1019340	0.87[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1019341	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1030069	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10459098	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10743982	0.87[ASW][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.94[YRI][hapmap];0.83[ASN][1000 genomes]
rs10743985	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10772563	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10772566	0.95[CHB][hapmap];0.89[ASN][1000 genomes]
rs10772567	0.94[CHB][hapmap];0.89[ASN][1000 genomes]
rs10845530	0.81[CHB][hapmap]
rs10845533	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10845537	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10845539	0.93[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10845540	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10845541	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10845542	0.89[ASN][1000 genomes]
rs10845544	0.94[CHB][hapmap];0.89[ASN][1000 genomes]
rs10845545	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10845546	0.88[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10845551	0.95[CHB][hapmap]
rs11054894	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11054914	0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs11532310	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11561172	0.88[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11609375	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11829916	0.82[ASN][1000 genomes]
rs1468876	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1544682	0.89[ASN][1000 genomes]
rs16908059	0.82[CHD][hapmap]
rs16908062	0.82[CHD][hapmap]
rs16908076	0.82[CHD][hapmap]
rs16908101	0.82[CHD][hapmap]
rs2160586	0.95[CHB][hapmap];0.94[CHD][hapmap];0.89[ASN][1000 genomes]
rs2193270	0.81[CHD][hapmap];0.89[JPT][hapmap]
rs2216264	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2417187	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3751261	0.89[CHB][hapmap]
rs3925170	0.87[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4390432	0.94[ASN][1000 genomes]
rs4488294	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4547192	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4763825	0.92[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4763826	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4763829	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4763830	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56701819	0.84[ASN][1000 genomes]
rs56915387	0.84[ASN][1000 genomes]
rs61543155	0.83[ASN][1000 genomes]
rs6488526	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7132512	0.81[CEU][hapmap];0.84[CHB][hapmap];0.89[TSI][hapmap];0.80[EUR][1000 genomes]
rs7135655	0.84[JPT][hapmap]
rs7295080	0.85[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7309503	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7309982	0.84[JPT][hapmap]
rs7310012	0.87[ASW][hapmap];0.82[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.94[YRI][hapmap];0.80[ASN][1000 genomes]
rs7311363	0.83[ASN][1000 genomes]
rs7311364	0.87[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7312010	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7315626	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7953025	0.81[ASW][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.94[YRI][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7954752	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7961703	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7967038	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7967111	0.92[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7967230	0.84[JPT][hapmap];0.88[MEX][hapmap]
rs7967466	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7969020	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7969252	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7969270	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7969849	0.88[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7969984	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs879445	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs888200	0.81[ASW][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9412	0.84[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949003	chr12:11938229-12618690	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv898810	chr12:12600080-12627410	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7313825	ETV6	cis	cerebellum	SCAN
rs7313825	ATF7IP	cis	cerebellum	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12590600-12614600	Weak transcription	Primary B cells from cord blood	blood
2	chr12:12594400-12618200	Weak transcription	Primary B cells from peripheral blood	blood
3	chr12:12595200-12609200	Weak transcription	GM12878-XiMat	blood
4	chr12:12595200-12618600	Weak transcription	Primary hematopoietic stem cells	blood
5	chr12:12596000-12620200	Weak transcription	HSMM	muscle
6	chr12:12596000-12629800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr12:12596200-12620600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr12:12596800-12618200	Weak transcription	Primary T cells from cord blood	blood
9	chr12:12596800-12618200	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr12:12597000-12617800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr12:12597400-12618200	Weak transcription	Gastric	stomach
12	chr12:12597400-12629000	Weak transcription	Rectal Smooth Muscle	rectum
13	chr12:12599000-12618600	Weak transcription	Left Ventricle	heart
14	chr12:12599600-12608600	Weak transcription	NHEK	skin
15	chr12:12600400-12609000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr12:12600600-12616800	Weak transcription	Fetal Stomach	stomach
17	chr12:12600800-12609000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr12:12600800-12610200	Weak transcription	Brain Anterior Caudate	brain
19	chr12:12601000-12609000	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr12:12601000-12620200	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr12:12602200-12610600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr12:12602600-12610600	Weak transcription	Brain Angular Gyrus	brain
23	chr12:12602800-12610000	Weak transcription	Brain Cingulate Gyrus	brain
24	chr12:12603200-12609200	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr12:12603200-12609400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr12:12603200-12609600	Weak transcription	Brain Substantia Nigra	brain
27	chr12:12603200-12618400	Weak transcription	Esophagus	oesophagus
28	chr12:12603400-12618600	Weak transcription	Pancreas	Pancrea
29	chr12:12603800-12614200	Weak transcription	Aorta	Aorta
30	chr12:12603800-12639200	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr12:12604000-12609400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr12:12604000-12628600	Weak transcription	Fetal Lung	lung
33	chr12:12604600-12608000	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr12:12604600-12609800	Weak transcription	Hela-S3	cervix
35	chr12:12604600-12613600	Weak transcription	Fetal Intestine Small	intestine
36	chr12:12604600-12618600	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr12:12605200-12618400	Weak transcription	Liver	Liver
38	chr12:12605400-12608000	Weak transcription	Fetal Intestine Large	intestine
39	chr12:12605600-12610400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr12:12606000-12609000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr12:12607200-12608400	Enhancers	Colon Smooth Muscle	Colon
42	chr12:12607200-12608600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr12:12607400-12608200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr12:12607600-12609400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr12:12607800-12608400	Enhancers	HepG2	liver
46	chr12:12607800-12629400	Weak transcription	Fetal Kidney	kidney

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links