Variant report

Variant	rs1052306
Chromosome Location	chr15:62149045-62149046
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:62148662..62150892-chr15:62154836..62157768,2	K562	blood:

Variant related genes	Relation type
ENSG00000129003	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs11071640	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11071644	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs11555593	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11555596	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11629559	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11629598	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs11629645	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs11629741	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11629851	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11629900	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs11631273	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes]
rs11632560	0.89[EUR][1000 genomes]
rs11634077	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs11634306	0.81[EUR][1000 genomes]
rs11634312	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11635880	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11636652	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11637606	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11637967	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11638455	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11639286	0.89[EUR][1000 genomes]
rs12148573	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12185103	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12898715	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12898859	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12901036	0.84[EUR][1000 genomes]
rs12901055	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12901735	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes]
rs12902859	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12905103	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12905264	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs12905403	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12907534	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12907567	1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12909386	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12911422	0.81[EUR][1000 genomes]
rs12912477	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes]
rs12913358	0.83[EUR][1000 genomes]
rs12915283	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12915585	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes]
rs12916410	0.87[EUR][1000 genomes]
rs17238096	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17271291	0.92[EUR][1000 genomes]
rs17303887	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17303894	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17303915	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2303405	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[EUR][1000 genomes]
rs34017665	0.83[EUR][1000 genomes]
rs34042779	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs34088392	0.89[EUR][1000 genomes]
rs34173668	0.83[EUR][1000 genomes]
rs34234705	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34257602	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs34282385	0.85[EUR][1000 genomes]
rs34424197	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs34435758	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34486946	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34556569	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs34589937	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34646089	1.00[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs34796280	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34853395	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34933463	0.85[EUR][1000 genomes]
rs34958705	0.89[EUR][1000 genomes]
rs34997975	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35259011	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs35324423	0.85[EUR][1000 genomes]
rs35523559	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35559361	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35607089	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35633657	0.84[EUR][1000 genomes]
rs35764401	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35984535	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs36004142	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs36056548	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs36126734	0.89[EUR][1000 genomes]
rs36175042	0.81[EUR][1000 genomes]
rs36185332	0.94[EUR][1000 genomes]
rs4143844	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs4143845	0.85[EUR][1000 genomes]
rs62006964	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs62006969	0.81[EUR][1000 genomes]
rs62007764	0.96[EUR][1000 genomes]
rs62007768	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs62007791	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs62009074	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62009078	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62009082	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62009106	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62009109	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs71411468	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71411469	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71411471	0.96[EUR][1000 genomes]
rs957348	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs978141	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1052306	VPS13C	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:62132400-62159000	Weak transcription	HSMM	muscle
2	chr15:62132400-62171200	Weak transcription	HMEC	breast
3	chr15:62135000-62161600	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr15:62136800-62150000	Weak transcription	HSMMtube	muscle
5	chr15:62138800-62184200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr15:62139200-62182200	Weak transcription	Brain Substantia Nigra	brain
7	chr15:62139400-62154800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr15:62139800-62185200	Weak transcription	NHLF	lung
9	chr15:62140000-62184800	Weak transcription	Right Ventricle	heart
10	chr15:62140200-62180000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr15:62141000-62149400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr15:62141200-62149600	Weak transcription	Psoas Muscle	Psoas
13	chr15:62141200-62165400	Weak transcription	Brain Hippocampus Middle	brain
14	chr15:62141400-62160600	Weak transcription	Placenta	Placenta
15	chr15:62141400-62161400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr15:62141600-62149200	Weak transcription	Ovary	ovary
17	chr15:62141600-62161400	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr15:62141600-62165000	Weak transcription	Thymus	Thymus
19	chr15:62141800-62149400	Weak transcription	Aorta	Aorta
20	chr15:62142000-62165000	Weak transcription	Gastric	stomach
21	chr15:62142000-62209400	Weak transcription	Colonic Mucosa	Colon
22	chr15:62142200-62161600	Weak transcription	Fetal Stomach	stomach
23	chr15:62142200-62162800	Weak transcription	Hela-S3	cervix
24	chr15:62142400-62160800	Weak transcription	Fetal Muscle Trunk	muscle
25	chr15:62142400-62163800	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr15:62142400-62253000	Weak transcription	Spleen	Spleen
27	chr15:62142600-62209200	Weak transcription	K562	blood
28	chr15:62143000-62164000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr15:62143200-62151800	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr15:62143200-62152400	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr15:62143800-62182200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr15:62143800-62235600	Weak transcription	Fetal Brain Male	brain
33	chr15:62144000-62159800	Weak transcription	Osteobl	bone
34	chr15:62144000-62194600	Weak transcription	Fetal Lung	lung
35	chr15:62144200-62149400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr15:62144200-62160600	Weak transcription	Fetal Thymus	thymus
37	chr15:62144400-62149400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr15:62144400-62149400	Weak transcription	Left Ventricle	heart
39	chr15:62144400-62153200	Weak transcription	Fetal Intestine Small	intestine
40	chr15:62144400-62155200	Weak transcription	Dnd41	blood
41	chr15:62144600-62154800	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr15:62144600-62155200	Weak transcription	A549	lung
43	chr15:62144800-62151400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr15:62144800-62161400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr15:62144800-62162400	Weak transcription	Rectal Smooth Muscle	rectum
46	chr15:62144800-62184000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr15:62145200-62149200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr15:62145200-62160600	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr15:62145200-62163400	Weak transcription	Brain Cingulate Gyrus	brain
50	chr15:62145200-62182000	Weak transcription	NHEK	skin

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