Variant report

Variant	rs17271312
Chromosome Location	chr15:62336279-62336280
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 97 )
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	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11629900	0.96[ASN][1000 genomes]
rs11631273	1.00[ASN][1000 genomes]
rs11632560	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11634077	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11634306	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11634312	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11634818	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11637599	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11637693	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11637967	0.86[ASN][1000 genomes]
rs11639286	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12148573	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[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	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12909673	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12911068	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12911422	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12913358	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12915585	0.92[ASN][1000 genomes]
rs12916410	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12917339	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17271291	0.96[ASN][1000 genomes]
rs2303405	0.92[ASN][1000 genomes]
rs34017665	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34042779	0.96[ASN][1000 genomes]
rs34088392	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34173668	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34234705	0.89[ASN][1000 genomes]
rs34257602	0.96[ASN][1000 genomes]
rs34282385	1.00[ASN][1000 genomes]
rs34311301	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34338090	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34391931	0.98[EUR][1000 genomes]
rs34424197	0.96[ASN][1000 genomes]
rs34435758	0.85[ASN][1000 genomes]
rs34486946	0.86[ASN][1000 genomes]
rs34546531	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34556569	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs34646089	1.00[ASN][1000 genomes]
rs34853395	0.85[ASN][1000 genomes]
rs34933463	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34958705	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35119291	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35168171	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35259011	0.96[ASN][1000 genomes]
rs35324423	0.88[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	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35932993	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35984535	0.82[ASN][1000 genomes]
rs36004142	0.89[ASN][1000 genomes]
rs36056548	0.85[ASN][1000 genomes]
rs36126734	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs36175042	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4143844	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4143845	0.83[AMR][1000 genomes]
rs62006964	0.96[ASN][1000 genomes]
rs62006969	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62007448	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62007453	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62007454	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62007455	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62007764	1.00[ASN][1000 genomes]
rs62007791	0.96[ASN][1000 genomes]
rs62008531	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[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:16 , 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	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
rs17271312	VPS13C	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:62244600-62350400	Weak transcription	Small Intestine	intestine
2	chr15:62265600-62338200	Weak transcription	Stomach Mucosa	stomach
3	chr15:62276400-62345000	Weak transcription	Colon Smooth Muscle	Colon
4	chr15:62288600-62336600	Weak transcription	Brain Cingulate Gyrus	brain
5	chr15:62300400-62351400	Weak transcription	Fetal Muscle Leg	muscle
6	chr15:62300600-62337600	Weak transcription	Fetal Stomach	stomach
7	chr15:62300600-62342400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr15:62300600-62345800	Weak transcription	Gastric	stomach
9	chr15:62300600-62351800	Weak transcription	Lung	lung
10	chr15:62300800-62351600	Weak transcription	Fetal Muscle Trunk	muscle
11	chr15:62302200-62351600	Weak transcription	Fetal Thymus	thymus
12	chr15:62302200-62351600	Weak transcription	Ovary	ovary
13	chr15:62306200-62343600	Weak transcription	Stomach Smooth Muscle	stomach
14	chr15:62313400-62337000	Weak transcription	Placenta	Placenta
15	chr15:62313400-62342800	Weak transcription	Left Ventricle	heart
16	chr15:62313400-62345600	Weak transcription	Brain Anterior Caudate	brain
17	chr15:62314800-62338000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr15:62315200-62338400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr15:62315200-62342600	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr15:62320000-62336600	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr15:62321200-62350800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr15:62322800-62338600	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr15:62326200-62337800	Weak transcription	Duodenum Mucosa	Duodenum
24	chr15:62326600-62337800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr15:62327800-62337600	Weak transcription	K562	blood
26	chr15:62328000-62345800	Weak transcription	Brain Hippocampus Middle	brain
27	chr15:62328000-62350000	Weak transcription	Brain Angular Gyrus	brain
28	chr15:62328200-62337600	Weak transcription	GM12878-XiMat	blood
29	chr15:62328200-62339800	Weak transcription	Hela-S3	cervix
30	chr15:62328200-62343600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr15:62328200-62350800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr15:62328400-62336800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr15:62328400-62350800	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr15:62328400-62351200	Weak transcription	NHLF	lung
35	chr15:62328400-62351400	Weak transcription	Osteobl	bone
36	chr15:62328600-62345000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr15:62328800-62342600	Weak transcription	A549	lung
38	chr15:62328800-62350000	Weak transcription	HUVEC	blood vessel
39	chr15:62328800-62350800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr15:62329000-62336600	Weak transcription	Fetal Brain Female	brain
41	chr15:62329000-62350400	Weak transcription	NHDF-Ad	bronchial
42	chr15:62330800-62348600	Weak transcription	Fetal Intestine Small	intestine
43	chr15:62332600-62337600	Weak transcription	Primary T cells from cord blood	blood
44	chr15:62332600-62338600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr15:62332600-62342400	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr15:62332600-62345400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr15:62333200-62336400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr15:62333200-62337000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr15:62333400-62338400	Weak transcription	Primary hematopoietic stem cells	blood
50	chr15:62333400-62351400	Weak transcription	Rectal Smooth Muscle	rectum

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