Variant report

Variant	rs17385059
Chromosome Location	chr15:77637812-77637813
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:77631784..77633576-chr15:77635603..77638413,2	MCF-7	breast:

Extended variants
information (count: 81 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10162742	0.85[YRI][hapmap]
rs10162778	0.82[ASN][1000 genomes]
rs11853696	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11854466	0.85[ASN][1000 genomes]
rs11856084	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11856513	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs11857330	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs11858844	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12324016	0.92[ASN][1000 genomes]
rs12324211	0.93[CHB][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs12324366	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs12324632	0.87[YRI][hapmap]
rs12324795	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12902446	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs12912084	0.90[ASN][1000 genomes]
rs13380202	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1374201	0.87[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.86[LWK][hapmap];0.97[TSI][hapmap]
rs1446313	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1493699	0.92[ASN][1000 genomes]
rs16968730	0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs16968799	0.92[ASN][1000 genomes]
rs16968897	0.90[CEU][hapmap];0.82[YRI][hapmap]
rs17384809	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17385296	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17385352	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17470529	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17470952	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17471252	0.83[ASN][1000 genomes]
rs17471431	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17471480	0.87[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.83[JPT][hapmap];0.90[MEX][hapmap];0.84[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17471697	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.87[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17471753	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17472200	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2012740	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2012756	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2137977	0.85[ASN][1000 genomes]
rs2172587	0.92[ASN][1000 genomes]
rs2292594	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[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]
rs2307141	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28437977	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2864840	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34572155	0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs35651077	0.92[ASN][1000 genomes]
rs3784787	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3784788	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4592615	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs4886857	0.85[ASN][1000 genomes]
rs4886863	0.90[ASN][1000 genomes]
rs4886864	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4886865	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56070388	0.81[ASN][1000 genomes]
rs58792939	0.81[ASN][1000 genomes]
rs59362734	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59386622	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60079927	0.85[ASN][1000 genomes]
rs62007297	0.88[ASN][1000 genomes]
rs62010566	0.92[ASN][1000 genomes]
rs7182221	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.85[ASN][1000 genomes]
rs74025104	0.81[ASN][1000 genomes]
rs74025105	0.85[ASN][1000 genomes]
rs74026910	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs74026912	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs74026913	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs74026918	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs74026923	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7496431	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs8029163	0.82[ASN][1000 genomes]
rs8035526	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs883627	0.83[JPT][hapmap]
rs907398	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040852	chr15:77160237-78137541	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1045376	chr15:77354671-77801487	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv542443	chr15:77354671-77801487	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription 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 target site	23 gene(s)	inside rSNPs	diseases
4	esv1832234	chr15:77451350-77694607	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv916323	chr15:77485765-78121259	Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv1051744	chr15:77511489-77679160	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	esv1830237	chr15:77535785-77694607	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv482689	chr15:77576396-77731559	Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv1040430	chr15:77584375-77676957	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	esv1836778	chr15:77608747-77694607	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	esv1795063	chr15:77628696-77697976	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17385059	CRABP1	cis	parietal	SCAN
rs17385059	HMG20A	cis	parietal	SCAN
rs17385059	TSPAN3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77620000-77645200	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr15:77620800-77639200	Weak transcription	Osteobl	bone
3	chr15:77622000-77645200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr15:77627400-77657400	Weak transcription	Aorta	Aorta
5	chr15:77628200-77638600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr15:77628200-77639200	Weak transcription	Fetal Lung	lung
7	chr15:77628200-77644600	Weak transcription	Right Atrium	heart
8	chr15:77628200-77655400	Weak transcription	Fetal Muscle Trunk	muscle
9	chr15:77628200-77655600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr15:77628400-77639000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr15:77628600-77646600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr15:77628800-77639400	Weak transcription	K562	blood
13	chr15:77628800-77645200	Weak transcription	NHLF	lung
14	chr15:77628800-77645400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr15:77629000-77639200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr15:77630800-77641800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr15:77630800-77645000	Weak transcription	NHDF-Ad	bronchial
18	chr15:77631200-77641800	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr15:77631800-77638600	Weak transcription	Left Ventricle	heart
20	chr15:77632200-77654800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr15:77633200-77639000	Weak transcription	HUVEC	blood vessel
22	chr15:77634000-77638400	Weak transcription	Primary B cells from cord blood	blood
23	chr15:77634000-77638800	Weak transcription	Psoas Muscle	Psoas
24	chr15:77634000-77639400	Weak transcription	Fetal Thymus	thymus
25	chr15:77634200-77639200	Weak transcription	Dnd41	blood
26	chr15:77634200-77644200	Weak transcription	Fetal Intestine Small	intestine
27	chr15:77635000-77655400	Weak transcription	HSMM	muscle
28	chr15:77635000-77657400	Weak transcription	Fetal Intestine Large	intestine
29	chr15:77635200-77638600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr15:77635200-77638600	Weak transcription	Brain Anterior Caudate	brain
31	chr15:77635200-77639600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr15:77635200-77655600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr15:77635400-77638400	Weak transcription	Brain Cingulate Gyrus	brain
34	chr15:77635400-77642000	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr15:77635400-77645200	Weak transcription	HSMMtube	muscle
36	chr15:77635600-77638800	Weak transcription	Brain Angular Gyrus	brain
37	chr15:77635600-77638800	Weak transcription	Brain Hippocampus Middle	brain
38	chr15:77635600-77639200	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr15:77635600-77639200	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr15:77635600-77639400	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr15:77635600-77643200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr15:77635800-77638800	Weak transcription	Fetal Heart	heart
43	chr15:77635800-77644600	Weak transcription	Ovary	ovary
44	chr15:77636600-77645600	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr15:77636800-77639400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr15:77636800-77658400	Weak transcription	Rectal Smooth Muscle	rectum
47	chr15:77637000-77638600	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr15:77637000-77643200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr15:77637200-77666800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr15:77637400-77639200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links