Variant report

Variant	rs2172587
Chromosome Location	chr15:77635234-77635235
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10162778	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11853696	0.88[ASN][1000 genomes]
rs11856084	0.93[CHB][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs11856513	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs11857330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs12324016	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12324211	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12324366	0.87[CHB][hapmap];0.94[JPT][hapmap]
rs12324795	0.86[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs12902446	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs12912084	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13380152	0.87[CHB][hapmap];0.94[JPT][hapmap]
rs13380202	0.92[ASN][1000 genomes]
rs1374201	0.93[CHB][hapmap];0.94[JPT][hapmap]
rs1446313	0.88[CHB][hapmap];0.94[JPT][hapmap]
rs1493699	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16968730	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs16968799	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17384809	0.92[ASN][1000 genomes]
rs17385059	0.92[ASN][1000 genomes]
rs17385296	0.88[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs17385352	0.92[ASN][1000 genomes]
rs17470529	0.90[ASN][1000 genomes]
rs17470952	0.86[ASN][1000 genomes]
rs17471252	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17471431	0.83[ASN][1000 genomes]
rs17471480	0.93[CHB][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs17471697	0.93[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs17471753	0.81[ASN][1000 genomes]
rs2012740	0.83[ASN][1000 genomes]
rs2012756	0.83[ASN][1000 genomes]
rs2292594	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs2307141	0.87[CHB][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs28437977	0.90[ASN][1000 genomes]
rs2864840	0.88[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs34572155	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs35651077	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3784787	0.90[ASN][1000 genomes]
rs3784788	0.88[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs4592615	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs4886863	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4886864	0.90[ASN][1000 genomes]
rs4886865	0.90[ASN][1000 genomes]
rs59362734	0.82[ASN][1000 genomes]
rs59386622	0.83[ASN][1000 genomes]
rs62007297	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62010566	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7163620	0.83[ASN][1000 genomes]
rs7182221	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs74026910	0.84[ASN][1000 genomes]
rs74026912	0.86[ASN][1000 genomes]
rs74026913	0.87[ASN][1000 genomes]
rs74026918	0.81[ASN][1000 genomes]
rs74026926	0.80[ASN][1000 genomes]
rs7496431	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs8029163	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8035526	0.90[ASN][1000 genomes]
rs883627	0.96[CEU][hapmap];0.83[JPT][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs907398	0.88[CHB][hapmap];0.83[JPT][hapmap]
rs9806326	0.82[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2172587	TSPAN3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:42 , 50 per page) page: 1

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	chr15:77622000-77636800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr15:77622000-77645200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr15:77627400-77657400	Weak transcription	Aorta	Aorta
6	chr15:77628200-77638600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr15:77628200-77639200	Weak transcription	Fetal Lung	lung
8	chr15:77628200-77644600	Weak transcription	Right Atrium	heart
9	chr15:77628200-77655400	Weak transcription	Fetal Muscle Trunk	muscle
10	chr15:77628200-77655600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr15:77628400-77639000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr15:77628600-77646600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr15:77628800-77639400	Weak transcription	K562	blood
14	chr15:77628800-77645200	Weak transcription	NHLF	lung
15	chr15:77628800-77645400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr15:77629000-77639200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr15:77630800-77635400	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr15:77630800-77641800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr15:77630800-77645000	Weak transcription	NHDF-Ad	bronchial
20	chr15:77631200-77641800	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr15:77631800-77638600	Weak transcription	Left Ventricle	heart
22	chr15:77632200-77654800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr15:77633200-77639000	Weak transcription	HUVEC	blood vessel
24	chr15:77634000-77638400	Weak transcription	Primary B cells from cord blood	blood
25	chr15:77634000-77638800	Weak transcription	Psoas Muscle	Psoas
26	chr15:77634000-77639400	Weak transcription	Fetal Thymus	thymus
27	chr15:77634200-77639200	Weak transcription	Dnd41	blood
28	chr15:77634200-77644200	Weak transcription	Fetal Intestine Small	intestine
29	chr15:77634400-77635400	Enhancers	Brain Cingulate Gyrus	brain
30	chr15:77634600-77635800	Enhancers	Fetal Heart	heart
31	chr15:77634800-77635600	Enhancers	Brain Hippocampus Middle	brain
32	chr15:77634800-77635600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
33	chr15:77635000-77635400	Enhancers	HSMMtube	muscle
34	chr15:77635000-77635600	Enhancers	Brain Angular Gyrus	brain
35	chr15:77635000-77635600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
36	chr15:77635000-77655400	Weak transcription	HSMM	muscle
37	chr15:77635000-77657400	Weak transcription	Fetal Intestine Large	intestine
38	chr15:77635200-77635600	Flanking Active TSS	Brain Substantia Nigra	brain
39	chr15:77635200-77638600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr15:77635200-77638600	Weak transcription	Brain Anterior Caudate	brain
41	chr15:77635200-77639600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr15:77635200-77655600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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