Variant report

Variant	rs34282385
Chromosome Location	chr15:62298949-62298950
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 131 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs1052306	0.85[EUR][1000 genomes]
rs11071640	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11071644	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11555593	0.87[EUR][1000 genomes]
rs11555596	0.85[EUR][1000 genomes]
rs11629559	0.87[EUR][1000 genomes]
rs11629598	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11629645	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11629741	0.87[EUR][1000 genomes]
rs11629851	0.89[EUR][1000 genomes]
rs11629900	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11631273	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11632560	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11634077	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11634306	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11634312	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11634818	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11635880	0.89[EUR][1000 genomes]
rs11636652	0.87[EUR][1000 genomes]
rs11637599	0.92[ASN][1000 genomes]
rs11637606	0.89[EUR][1000 genomes]
rs11637693	1.00[ASN][1000 genomes]
rs11637967	0.86[ASN][1000 genomes]
rs11638455	0.81[EUR][1000 genomes]
rs11639286	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12148573	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12185103	0.89[EUR][1000 genomes]
rs12901036	1.00[ASN][1000 genomes]
rs12901055	0.89[EUR][1000 genomes]
rs12901735	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12902859	0.87[EUR][1000 genomes]
rs12905103	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12905264	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12905403	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12907534	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12907567	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12909386	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12909673	1.00[ASN][1000 genomes]
rs12911068	0.81[EUR][1000 genomes]
rs12911422	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12912477	0.89[EUR][1000 genomes]
rs12913358	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12915283	0.89[EUR][1000 genomes]
rs12915585	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12916410	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12917339	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17238096	0.85[EUR][1000 genomes]
rs17271291	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17271312	1.00[ASN][1000 genomes]
rs17303887	0.87[EUR][1000 genomes]
rs17303894	0.85[EUR][1000 genomes]
rs17303915	0.89[EUR][1000 genomes]
rs2303405	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34017665	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34042779	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34088392	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34173668	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34234705	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34257602	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34311301	1.00[ASN][1000 genomes]
rs34424197	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34435758	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34486946	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34546531	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34556569	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34589937	0.87[EUR][1000 genomes]
rs34646089	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34796280	0.87[EUR][1000 genomes]
rs34853395	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34933463	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34958705	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34997975	0.87[EUR][1000 genomes]
rs35119291	1.00[ASN][1000 genomes]
rs35259011	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35324423	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35523559	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35559361	0.87[EUR][1000 genomes]
rs35607089	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35633657	1.00[ASN][1000 genomes]
rs35764401	0.85[EUR][1000 genomes]
rs35785804	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35932993	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35984535	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs36004142	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36056548	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs36126734	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36175042	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36185332	0.87[EUR][1000 genomes]
rs4143844	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4143845	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62006964	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62006969	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62007448	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62007764	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62007768	0.83[EUR][1000 genomes]
rs62007791	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62009074	0.87[EUR][1000 genomes]
rs62009078	0.87[EUR][1000 genomes]
rs62009082	0.89[EUR][1000 genomes]
rs62009106	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62009109	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs71411468	0.89[EUR][1000 genomes]
rs71411469	0.89[EUR][1000 genomes]
rs71411471	0.89[EUR][1000 genomes]
rs957348	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs978141	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:25 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521334	chr15:62129809-62340126	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv527451	chr15:62129809-62340126	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv904286	chr15:62146598-62313373	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv904287	chr15:62146598-62338797	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
5	nsv904288	chr15:62146598-62356386	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
6	nsv516639	chr15:62175134-62340126	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv904290	chr15:62175134-62356386	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv904292	chr15:62178695-62313373	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv904293	chr15:62178695-62338797	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv904294	chr15:62178695-62356386	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv457176	chr15:62178695-62519658	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
12	nsv569643	chr15:62178695-62519658	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
13	nsv904296	chr15:62198564-62313373	ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
14	nsv471247	chr15:62202481-62519658	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
15	nsv904297	chr15:62202482-62313373	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
16	nsv569645	chr15:62202482-62319307	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
17	nsv569646	chr15:62202482-62519658	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
18	nsv904298	chr15:62218689-62338797	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
19	nsv569648	chr15:62239697-62340126	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
20	nsv457177	chr15:62243197-62301094	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
21	nsv569649	chr15:62243197-62301094	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
22	nsv569650	chr15:62243197-62313373	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
23	nsv569651	chr15:62243197-62313417	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
24	nsv1044748	chr15:62276183-62521856	Active TSS Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
25	nsv542405	chr15:62276183-62521856	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Strong transcription 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	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs34282385	VPS13C	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:62185600-62333600	Weak transcription	Right Ventricle	heart
2	chr15:62185800-62300000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr15:62188600-62309400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr15:62221400-62327600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr15:62230800-62317200	Weak transcription	Pancreas	Pancrea
6	chr15:62244600-62350400	Weak transcription	Small Intestine	intestine
7	chr15:62254000-62303600	Weak transcription	Spleen	Spleen
8	chr15:62259400-62327200	Weak transcription	HepG2	liver
9	chr15:62262600-62312600	Weak transcription	NHEK	skin
10	chr15:62264000-62312600	Weak transcription	Rectal Smooth Muscle	rectum
11	chr15:62264000-62323800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr15:62264000-62324000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr15:62264800-62299400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr15:62265000-62299400	Weak transcription	Brain Germinal Matrix	brain
15	chr15:62265000-62299800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr15:62265600-62299600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr15:62265600-62338200	Weak transcription	Stomach Mucosa	stomach
18	chr15:62265800-62299200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr15:62266000-62299200	Weak transcription	Fetal Kidney	kidney
20	chr15:62267600-62299800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr15:62271200-62299200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr15:62273600-62300400	Weak transcription	Fetal Muscle Trunk	muscle
23	chr15:62274800-62299000	Weak transcription	NH-A	brain
24	chr15:62276400-62299000	Weak transcription	HSMMtube	muscle
25	chr15:62276400-62299200	Weak transcription	Hela-S3	cervix
26	chr15:62276400-62299400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr15:62276400-62326800	Weak transcription	Thymus	Thymus
28	chr15:62276400-62345000	Weak transcription	Colon Smooth Muscle	Colon
29	chr15:62276600-62299800	Weak transcription	Fetal Muscle Leg	muscle
30	chr15:62276600-62299800	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr15:62276600-62327600	Weak transcription	NHLF	lung
32	chr15:62276800-62299400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr15:62276800-62317000	Weak transcription	Psoas Muscle	Psoas
34	chr15:62278000-62302000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr15:62278400-62299200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr15:62278400-62299400	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr15:62280000-62299600	Weak transcription	Fetal Thymus	thymus
38	chr15:62282200-62306600	Weak transcription	Brain Substantia Nigra	brain
39	chr15:62282200-62319000	Weak transcription	Fetal Brain Female	brain
40	chr15:62282200-62327800	Weak transcription	Colonic Mucosa	Colon
41	chr15:62282400-62299000	Weak transcription	HUVEC	blood vessel
42	chr15:62282400-62314200	Weak transcription	Fetal Brain Male	brain
43	chr15:62282600-62299400	Weak transcription	A549	lung
44	chr15:62283200-62299000	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr15:62283600-62299200	Weak transcription	NHDF-Ad	bronchial
46	chr15:62284600-62299400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr15:62287200-62299000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr15:62287200-62299000	Weak transcription	Osteobl	bone
49	chr15:62287400-62322200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr15:62288000-62299200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links