Variant report

Variant	rs12916410
Chromosome Location	chr15:62302886-62302887
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:62266682..62269656-chr15:62302600..62304271,2	K562	blood:

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

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs1052306	0.87[EUR][1000 genomes]
rs11071640	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11071644	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11555593	0.89[EUR][1000 genomes]
rs11555596	0.87[EUR][1000 genomes]
rs11629559	0.89[EUR][1000 genomes]
rs11629598	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11629645	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11629741	0.89[EUR][1000 genomes]
rs11629851	0.91[EUR][1000 genomes]
rs11629900	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11631273	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11632560	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11634077	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11634306	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11634312	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11634818	0.89[AMR][1000 genomes]
rs11635880	0.91[EUR][1000 genomes]
rs11636652	0.89[EUR][1000 genomes]
rs11637599	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11637606	0.91[EUR][1000 genomes]
rs11637693	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11637967	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11638455	0.83[EUR][1000 genomes]
rs11639286	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12148573	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12185103	0.91[EUR][1000 genomes]
rs12901036	1.00[ASN][1000 genomes]
rs12901055	0.91[EUR][1000 genomes]
rs12901735	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12902859	0.89[EUR][1000 genomes]
rs12905103	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12905264	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12905403	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12907534	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12907567	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12909386	0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12909673	1.00[ASN][1000 genomes]
rs12911068	0.83[EUR][1000 genomes]
rs12911422	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12912477	0.91[EUR][1000 genomes]
rs12913358	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12915283	0.91[EUR][1000 genomes]
rs12915585	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12917339	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17238096	0.87[EUR][1000 genomes]
rs17271291	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17271312	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17303887	0.89[EUR][1000 genomes]
rs17303894	0.87[EUR][1000 genomes]
rs17303915	0.91[EUR][1000 genomes]
rs2303405	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34017665	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34042779	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34088392	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34173668	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34234705	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34257602	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34282385	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34311301	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34424197	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34435758	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34486946	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34546531	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34556569	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34589937	0.89[EUR][1000 genomes]
rs34646089	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34796280	0.89[EUR][1000 genomes]
rs34853395	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34933463	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34958705	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34997975	0.89[EUR][1000 genomes]
rs35119291	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35259011	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35324423	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35523559	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35559361	0.89[EUR][1000 genomes]
rs35607089	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35633657	1.00[ASN][1000 genomes]
rs35764401	0.87[EUR][1000 genomes]
rs35785804	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35932993	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35984535	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs36004142	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36056548	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs36126734	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36175042	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36185332	0.89[EUR][1000 genomes]
rs4143844	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4143845	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62006964	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62006969	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62007448	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62007453	0.83[AMR][1000 genomes]
rs62007764	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62007768	0.85[EUR][1000 genomes]
rs62007791	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62008531	0.83[AMR][1000 genomes]
rs62009074	0.89[EUR][1000 genomes]
rs62009078	0.89[EUR][1000 genomes]
rs62009082	0.91[EUR][1000 genomes]
rs62009106	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62009109	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs71411468	0.91[EUR][1000 genomes]
rs71411469	0.91[EUR][1000 genomes]
rs71411471	0.91[EUR][1000 genomes]
rs957348	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs978141	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 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	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
21	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
22	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
23	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
rs12916410	VPS13C	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:110 , 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	chr15:62188600-62309400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr15:62221400-62327600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr15:62230800-62317200	Weak transcription	Pancreas	Pancrea
5	chr15:62244600-62350400	Weak transcription	Small Intestine	intestine
6	chr15:62254000-62303600	Weak transcription	Spleen	Spleen
7	chr15:62259400-62327200	Weak transcription	HepG2	liver
8	chr15:62262600-62312600	Weak transcription	NHEK	skin
9	chr15:62264000-62312600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr15:62264000-62323800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr15:62264000-62324000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr15:62265600-62338200	Weak transcription	Stomach Mucosa	stomach
13	chr15:62276400-62326800	Weak transcription	Thymus	Thymus
14	chr15:62276400-62345000	Weak transcription	Colon Smooth Muscle	Colon
15	chr15:62276600-62327600	Weak transcription	NHLF	lung
16	chr15:62276800-62317000	Weak transcription	Psoas Muscle	Psoas
17	chr15:62282200-62306600	Weak transcription	Brain Substantia Nigra	brain
18	chr15:62282200-62319000	Weak transcription	Fetal Brain Female	brain
19	chr15:62282200-62327800	Weak transcription	Colonic Mucosa	Colon
20	chr15:62282400-62314200	Weak transcription	Fetal Brain Male	brain
21	chr15:62287400-62322200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr15:62288600-62327600	Weak transcription	HMEC	breast
23	chr15:62288600-62336600	Weak transcription	Brain Cingulate Gyrus	brain
24	chr15:62291000-62312400	Weak transcription	Left Ventricle	heart
25	chr15:62293600-62304000	Weak transcription	HSMM	muscle
26	chr15:62297000-62315000	Weak transcription	K562	blood
27	chr15:62298000-62307200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr15:62298000-62307400	Strong transcription	Primary T helper cells PMA-I stimulated	--
29	chr15:62298000-62307400	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr15:62298200-62314000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr15:62298400-62307000	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr15:62299000-62303000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr15:62299000-62303400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr15:62299000-62306800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr15:62299000-62307200	Strong transcription	Primary B cells from peripheral blood	blood
36	chr15:62299000-62307400	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr15:62299000-62307400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr15:62299000-62307800	Strong transcription	Primary B cells from cord blood	blood
39	chr15:62299200-62306000	Strong transcription	NHDF-Ad	bronchial
40	chr15:62299200-62306200	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr15:62299200-62306200	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr15:62299200-62307200	Strong transcription	Liver	Liver
43	chr15:62299200-62307200	Strong transcription	Rectal Mucosa Donor 31	rectum
44	chr15:62299400-62303200	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr15:62299400-62303200	Strong transcription	Placenta	Placenta
46	chr15:62299800-62303200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr15:62299800-62307400	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr15:62300000-62305000	Strong transcription	GM12878-XiMat	blood
49	chr15:62300000-62307200	Strong transcription	Dnd41	blood
50	chr15:62300000-62307400	Weak transcription	HUES6 Cell Line	embryonic stem cell

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