Variant report

Variant	rs12917339
Chromosome Location	chr15:62346790-62346791
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:62343215..62348016-chr15:62348672..62353157,7	K562	blood:
2	chr15:62346359..62349999-chr15:62351464..62353902,5	MCF-7	breast:
3	chr15:62320983..62322579-chr15:62345142..62347207,2	K562	blood:
4	chr15:62346399..62348627-chr15:62350177..62352518,4	MCF-7	breast:
5	chr15:62344281..62348307-chr15:62349170..62353134,6	K562	blood:

Variant related genes	Relation type
ENSG00000129003	Chromatin interaction
ENSG00000259251	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs11071640	0.82[ASN][1000 genomes]
rs11071644	1.00[ASN][1000 genomes]
rs11629598	1.00[ASN][1000 genomes]
rs11629645	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11629900	0.96[ASN][1000 genomes]
rs11631273	1.00[ASN][1000 genomes]
rs11632560	1.00[ASN][1000 genomes]
rs11634077	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11634306	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11634312	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11634818	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11637599	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11637693	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11637967	0.86[ASN][1000 genomes]
rs11639286	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12148573	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12901036	1.00[ASN][1000 genomes]
rs12901735	0.96[ASN][1000 genomes]
rs12905103	0.89[ASN][1000 genomes]
rs12905264	0.96[ASN][1000 genomes]
rs12905403	0.89[ASN][1000 genomes]
rs12907534	0.85[ASN][1000 genomes]
rs12907567	0.89[ASN][1000 genomes]
rs12909386	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12909673	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12911068	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12911422	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12913358	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12915585	0.92[ASN][1000 genomes]
rs12916410	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17271291	0.96[ASN][1000 genomes]
rs17271312	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2303405	0.92[ASN][1000 genomes]
rs34017665	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34042779	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs34088392	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34173668	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34234705	0.89[ASN][1000 genomes]
rs34257602	0.96[ASN][1000 genomes]
rs34282385	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34311301	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34338090	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34391931	0.96[EUR][1000 genomes]
rs34424197	0.96[ASN][1000 genomes]
rs34435758	0.85[ASN][1000 genomes]
rs34486946	0.86[ASN][1000 genomes]
rs34546531	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34556569	0.96[ASN][1000 genomes]
rs34646089	1.00[ASN][1000 genomes]
rs34853395	0.85[ASN][1000 genomes]
rs34933463	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34958705	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35119291	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35168171	0.90[EUR][1000 genomes]
rs35259011	0.96[ASN][1000 genomes]
rs35324423	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35523559	0.89[ASN][1000 genomes]
rs35607089	0.85[ASN][1000 genomes]
rs35633657	1.00[ASN][1000 genomes]
rs35785804	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35932993	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35984535	0.82[ASN][1000 genomes]
rs36004142	0.89[ASN][1000 genomes]
rs36056548	0.85[ASN][1000 genomes]
rs36126734	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs36175042	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4143844	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4143845	0.89[AMR][1000 genomes]
rs62006964	0.96[ASN][1000 genomes]
rs62006969	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62007448	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62007453	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62007454	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62007455	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62007764	1.00[ASN][1000 genomes]
rs62007791	0.96[ASN][1000 genomes]
rs62008531	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62009106	0.89[ASN][1000 genomes]
rs62009109	0.86[ASN][1000 genomes]
rs957348	0.85[ASN][1000 genomes]
rs978141	0.96[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	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	nsv457178	chr15:62340126-62394324	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
11	nsv569652	chr15:62340126-62394324	Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12917339	VPS13C	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:62244600-62350400	Weak transcription	Small Intestine	intestine
2	chr15:62300400-62351400	Weak transcription	Fetal Muscle Leg	muscle
3	chr15:62300600-62351800	Weak transcription	Lung	lung
4	chr15:62300800-62351600	Weak transcription	Fetal Muscle Trunk	muscle
5	chr15:62302200-62351600	Weak transcription	Fetal Thymus	thymus
6	chr15:62302200-62351600	Weak transcription	Ovary	ovary
7	chr15:62321200-62350800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr15:62328000-62350000	Weak transcription	Brain Angular Gyrus	brain
9	chr15:62328200-62350800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr15:62328400-62350800	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr15:62328400-62351200	Weak transcription	NHLF	lung
12	chr15:62328400-62351400	Weak transcription	Osteobl	bone
13	chr15:62328800-62350000	Weak transcription	HUVEC	blood vessel
14	chr15:62328800-62350800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr15:62329000-62350400	Weak transcription	NHDF-Ad	bronchial
16	chr15:62330800-62348600	Weak transcription	Fetal Intestine Small	intestine
17	chr15:62333400-62351400	Weak transcription	Rectal Smooth Muscle	rectum
18	chr15:62333600-62351400	Weak transcription	HSMM	muscle
19	chr15:62333800-62350600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr15:62336000-62350400	Weak transcription	Fetal Intestine Large	intestine
21	chr15:62339600-62350800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr15:62342200-62351400	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr15:62342600-62347600	Enhancers	Primary neutrophils fromperipheralblood	blood
24	chr15:62343000-62350600	Weak transcription	K562	blood
25	chr15:62343800-62348400	Enhancers	Primary T helper cells fromperipheralblood	blood
26	chr15:62344000-62350400	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr15:62344000-62350800	Weak transcription	Brain Cingulate Gyrus	brain
28	chr15:62344000-62350800	Weak transcription	Left Ventricle	heart
29	chr15:62344000-62350800	Weak transcription	Stomach Smooth Muscle	stomach
30	chr15:62344000-62351200	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr15:62344800-62347200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr15:62344800-62348200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr15:62344800-62348400	Enhancers	Primary T helper cells PMA-I stimulated	--
34	chr15:62345000-62347200	Enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr15:62345000-62347600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
36	chr15:62345000-62348200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr15:62345000-62348200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
38	chr15:62345000-62348200	Enhancers	HepG2	liver
39	chr15:62345000-62348400	Enhancers	Primary T helper naive cells from peripheral blood	blood
40	chr15:62345200-62347200	Enhancers	Pancreatic Islets	Pancreatic Islet
41	chr15:62345600-62346800	Enhancers	Brain Anterior Caudate	brain
42	chr15:62345600-62347000	Weak transcription	A549	lung
43	chr15:62345600-62348000	Enhancers	Monocytes-CD14+_RO01746	blood
44	chr15:62345600-62349800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr15:62345600-62349800	Weak transcription	Colon Smooth Muscle	Colon
46	chr15:62345600-62351400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr15:62345800-62346800	Enhancers	Gastric	stomach
48	chr15:62345800-62351000	Weak transcription	Fetal Lung	lung
49	chr15:62346000-62346800	Enhancers	GM12878-XiMat	blood
50	chr15:62346000-62350000	Weak transcription	Duodenum Mucosa	Duodenum

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