Variant report

Variant	rs7315820
Chromosome Location	chr12:48598938-48598939
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:48597340..48600068-chr12:48604806..48607585,2	MCF-7	breast:

Extended variants
information (count: 71 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10875719	0.81[GIH][hapmap]
rs10875743	1.00[CHB][hapmap]
rs10875749	1.00[CHB][hapmap]
rs10875753	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap]
rs10875763	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1107654	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.80[YRI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168408	1.00[CHB][hapmap]
rs11168428	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap]
rs11168437	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap]
rs11168441	1.00[CHB][hapmap];0.83[AFR][1000 genomes]
rs11168460	1.00[CHB][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168464	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168468	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168474	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168484	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12228750	1.00[CHB][hapmap]
rs12368659	1.00[CHB][hapmap];0.83[AFR][1000 genomes]
rs12816820	1.00[CHB][hapmap]
rs12828309	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12829841	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1387259	0.83[EUR][1000 genomes]
rs1387260	0.83[EUR][1000 genomes]
rs1476607	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap]
rs1542707	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1552550	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2054905	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[YRI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2450994	0.92[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs2468943	0.88[CEU][hapmap];0.88[GIH][hapmap];0.84[TSI][hapmap]
rs2634681	0.92[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs2634684	0.92[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs2634693	0.80[EUR][1000 genomes]
rs2634697	1.00[ASN][1000 genomes]
rs2732441	0.92[CEU][hapmap]
rs2732445	1.00[ASN][1000 genomes]
rs2732448	0.92[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs2732457	0.92[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap]
rs2732461	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs2732462	0.83[EUR][1000 genomes]
rs2732466	0.92[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs2732480	0.90[GIH][hapmap];0.85[MEX][hapmap]
rs2732481	0.92[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap]
rs2732484	0.92[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs2956703	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2956710	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3087716	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs34286639	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4760612	1.00[CHB][hapmap]
rs4760679	1.00[CHB][hapmap]
rs6580650	0.83[GIH][hapmap]
rs6580662	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7139330	1.00[CHB][hapmap]
rs7297824	1.00[CEU][hapmap];1.00[CHB][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]
rs7301003	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap]
rs7307566	1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7486941	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7487682	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.85[MEX][hapmap];0.89[MKK][hapmap];0.87[TSI][hapmap]
rs7959684	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs7966829	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7975632	1.00[CHB][hapmap];0.83[GIH][hapmap]
rs8716	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap]
rs923397	0.92[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs973398	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers 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	57 gene(s)	inside rSNPs	diseases
3	nsv8971	chr12:48536526-48758501	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Active 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	39 gene(s)	inside rSNPs	diseases
4	esv34439	chr12:48541757-48779562	Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	esv2757502	chr12:48547128-48779562	Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	esv33956	chr12:48565643-48645561	Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv976031	chr12:48594968-48610975	Enhancers Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv976038	chr12:48596152-48610975	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv518743	chr12:48597507-48600520	ZNF genes & repeats Weak transcription Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs7315820	ENST00000266592	cis	multi-tissue	Pritchard
rs7315820	ZNF641	cis	multi-tissue	Pritchard
rs7315820	ZNF641	cis	Liver	GTEx
rs7315820	H1FNT	cis	Muscle Skeletal	GTEx
rs7315820	FXN	trans	multi-tissue	Pritchard
rs7315820	FKBP11	cis	cerebellum	SCAN
rs7315820	ZNF641	cis	cerebellum	SCAN
rs7315820	FXN	cis	Liver	GTEx

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48592800-48600400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:48593200-48599000	Weak transcription	Brain Angular Gyrus	brain
3	chr12:48593200-48600200	Weak transcription	Right Ventricle	heart
4	chr12:48593400-48600800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr12:48594800-48599000	Weak transcription	Rectal Smooth Muscle	rectum
6	chr12:48595200-48600400	Weak transcription	Psoas Muscle	Psoas
7	chr12:48595600-48609600	Weak transcription	Placenta	Placenta
8	chr12:48595800-48599600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr12:48595800-48600800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr12:48596000-48599600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr12:48596600-48603800	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr12:48597000-48606600	Weak transcription	Left Ventricle	heart
13	chr12:48597000-48606800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr12:48597800-48599200	ZNF genes & repeats	Stomach Smooth Muscle	stomach
15	chr12:48598000-48599600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
16	chr12:48598200-48599200	ZNF genes & repeats	Brain Anterior Caudate	brain
17	chr12:48598400-48599000	ZNF genes & repeats	Primary T helper 17 cells PMA-I stimulated	--
18	chr12:48598400-48599000	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
19	chr12:48598400-48599200	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
20	chr12:48598400-48599200	ZNF genes & repeats	Adipose Nuclei	Adipose
21	chr12:48598400-48599200	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
22	chr12:48598400-48599400	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
23	chr12:48598400-48599400	Strong transcription	Brain Cingulate Gyrus	brain
24	chr12:48598400-48599400	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
25	chr12:48598400-48599400	Strong transcription	Skeletal Muscle Female	skeletal muscle
26	chr12:48598400-48599600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
27	chr12:48598400-48600200	Weak transcription	Brain Hippocampus Middle	brain
28	chr12:48598600-48599000	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr12:48598600-48599000	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
30	chr12:48598600-48599200	ZNF genes & repeats	Brain Substantia Nigra	brain
31	chr12:48598600-48599200	ZNF genes & repeats	Fetal Muscle Leg	muscle
32	chr12:48598600-48599400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
33	chr12:48598600-48599400	ZNF genes & repeats	Primary T helper naive cells from peripheral blood	blood
34	chr12:48598600-48599400	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
35	chr12:48598600-48599400	ZNF genes & repeats	Colon Smooth Muscle	Colon
36	chr12:48598600-48599800	ZNF genes & repeats	Ovary	ovary
37	chr12:48598800-48599000	ZNF genes & repeats	Fetal Lung	lung
38	chr12:48598800-48599200	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr12:48598800-48599400	ZNF genes & repeats	Fetal Heart	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links