Variant report

Variant	rs34796280
Chromosome Location	chr15:62185879-62185880
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 111 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs1052306	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11071640	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11071644	0.88[EUR][1000 genomes]
rs11555593	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11555596	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11629559	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11629598	0.96[EUR][1000 genomes]
rs11629645	0.85[EUR][1000 genomes]
rs11629741	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11629851	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11629900	1.00[EUR][1000 genomes]
rs11631273	1.00[EUR][1000 genomes]
rs11632560	0.91[EUR][1000 genomes]
rs11634077	0.83[EUR][1000 genomes]
rs11634306	0.83[EUR][1000 genomes]
rs11635880	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11636652	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11637606	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11637967	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11638455	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11639286	0.91[EUR][1000 genomes]
rs12185103	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12898715	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12898859	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12901036	0.86[EUR][1000 genomes]
rs12901055	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12901735	0.98[EUR][1000 genomes]
rs12902859	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12905103	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12905264	0.92[EUR][1000 genomes]
rs12905403	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12907534	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12907567	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12911422	0.83[EUR][1000 genomes]
rs12912477	0.98[EUR][1000 genomes]
rs12913358	0.85[EUR][1000 genomes]
rs12915283	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12915585	1.00[EUR][1000 genomes]
rs12916410	0.89[EUR][1000 genomes]
rs17238096	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17271291	0.94[EUR][1000 genomes]
rs17303887	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17303894	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17303915	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2303405	1.00[EUR][1000 genomes]
rs34017665	0.85[EUR][1000 genomes]
rs34042779	0.92[EUR][1000 genomes]
rs34088392	0.91[EUR][1000 genomes]
rs34173668	0.85[EUR][1000 genomes]
rs34234705	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34257602	0.94[EUR][1000 genomes]
rs34282385	0.87[EUR][1000 genomes]
rs34424197	0.94[EUR][1000 genomes]
rs34435758	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34486946	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34556569	0.94[EUR][1000 genomes]
rs34589937	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34646089	1.00[EUR][1000 genomes]
rs34853395	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34933463	0.87[EUR][1000 genomes]
rs34958705	0.91[EUR][1000 genomes]
rs34997975	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35259011	0.94[EUR][1000 genomes]
rs35324423	0.87[EUR][1000 genomes]
rs35523559	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35559361	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35607089	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35633657	0.86[EUR][1000 genomes]
rs35764401	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35984535	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs36004142	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36056548	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs36126734	0.91[EUR][1000 genomes]
rs36175042	0.83[EUR][1000 genomes]
rs36185332	0.96[EUR][1000 genomes]
rs4143844	0.85[EUR][1000 genomes]
rs4143845	0.87[EUR][1000 genomes]
rs62006964	0.94[EUR][1000 genomes]
rs62006969	0.83[EUR][1000 genomes]
rs62007448	0.82[EUR][1000 genomes]
rs62007764	0.98[EUR][1000 genomes]
rs62007768	0.96[EUR][1000 genomes]
rs62007791	0.94[EUR][1000 genomes]
rs62009074	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62009078	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62009082	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62009106	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62009109	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71411468	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71411469	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71411471	0.98[EUR][1000 genomes]
rs957348	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs978141	0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904284	chr15:62123600-62243197	Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	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
3	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
4	nsv904285	chr15:62146598-62246864	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	nsv569641	chr15:62155282-62287456	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
9	nsv904289	chr15:62156690-62287456	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
10	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
11	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
12	nsv569642	chr15:62178695-62243197	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv904291	chr15:62178695-62287456	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	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
15	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
16	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
17	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
18	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs34796280	VPS13C	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:62142000-62209400	Weak transcription	Colonic Mucosa	Colon
2	chr15:62142400-62253000	Weak transcription	Spleen	Spleen
3	chr15:62142600-62209200	Weak transcription	K562	blood
4	chr15:62143800-62235600	Weak transcription	Fetal Brain Male	brain
5	chr15:62144000-62194600	Weak transcription	Fetal Lung	lung
6	chr15:62146800-62230000	Weak transcription	Pancreas	Pancrea
7	chr15:62149000-62198000	Weak transcription	Fetal Kidney	kidney
8	chr15:62150000-62276200	Weak transcription	Psoas Muscle	Psoas
9	chr15:62154200-62198200	Weak transcription	NH-A	brain
10	chr15:62162600-62195200	Weak transcription	Fetal Stomach	stomach
11	chr15:62163000-62198400	Weak transcription	Osteobl	bone
12	chr15:62165600-62198400	Weak transcription	Thymus	Thymus
13	chr15:62173400-62198200	Weak transcription	Left Ventricle	heart
14	chr15:62181800-62186000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr15:62181800-62198800	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr15:62182600-62197200	Weak transcription	HSMM	muscle
17	chr15:62182600-62198400	Weak transcription	Fetal Thymus	thymus
18	chr15:62183000-62198200	Weak transcription	HUVEC	blood vessel
19	chr15:62184000-62186400	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
20	chr15:62184000-62187600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr15:62184000-62190000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr15:62184000-62190000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr15:62184200-62186400	ZNF genes & repeats	Placenta	Placenta
24	chr15:62184200-62186600	ZNF genes & repeats	Fetal Intestine Small	intestine
25	chr15:62184200-62187200	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
26	chr15:62184200-62187600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr15:62184200-62188000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr15:62184200-62188200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
29	chr15:62184400-62186200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr15:62184400-62186200	ZNF genes & repeats	Primary B cells from cord blood	blood
31	chr15:62184400-62186800	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
32	chr15:62184400-62187000	ZNF genes & repeats	Primary B cells from peripheral blood	blood
33	chr15:62184400-62187200	ZNF genes & repeats	Adipose Nuclei	Adipose
34	chr15:62184400-62187200	ZNF genes & repeats	GM12878-XiMat	blood
35	chr15:62184600-62186000	ZNF genes & repeats	Brain Anterior Caudate	brain
36	chr15:62184600-62187000	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
37	chr15:62184600-62187000	ZNF genes & repeats	Fetal Intestine Large	intestine
38	chr15:62184600-62187400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr15:62184600-62188000	ZNF genes & repeats	Primary T cells from cord blood	blood
40	chr15:62184600-62236800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr15:62184800-62186000	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr15:62184800-62186000	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 2	blood
43	chr15:62184800-62186200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
44	chr15:62184800-62186200	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
45	chr15:62184800-62186200	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
46	chr15:62184800-62186400	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
47	chr15:62185000-62187200	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
48	chr15:62185000-62187400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
49	chr15:62185000-62199600	Weak transcription	Stomach Mucosa	stomach
50	chr15:62185000-62221000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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