Variant report

Variant	rs35559361
Chromosome Location	chr15:62183517-62183518
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	chr15:62170697..62173317-chr15:62182241..62184749,2	MCF-7	breast:

Extended variants
information (count: 110 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs1052306	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11071640	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11071644	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs11555593	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11555596	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11629559	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11629598	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs11629645	0.81[EUR][1000 genomes]
rs11629741	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11629851	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11629900	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs11631273	0.96[EUR][1000 genomes]
rs11632560	0.87[EUR][1000 genomes]
rs11634077	0.84[EUR][1000 genomes]
rs11634306	0.84[EUR][1000 genomes]
rs11635880	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11636652	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11637606	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11637967	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11638455	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11639286	0.87[EUR][1000 genomes]
rs12185103	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12898715	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12898859	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12901036	0.83[EUR][1000 genomes]
rs12901055	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12901735	0.98[EUR][1000 genomes]
rs12902859	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12905103	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12905264	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs12905403	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12907534	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12907567	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12912477	0.98[EUR][1000 genomes]
rs12913358	0.81[EUR][1000 genomes]
rs12915283	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12915585	0.96[EUR][1000 genomes]
rs12916410	0.89[EUR][1000 genomes]
rs17238096	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17271291	0.90[EUR][1000 genomes]
rs17303887	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17303894	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17303915	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2303405	0.96[EUR][1000 genomes]
rs34017665	0.85[EUR][1000 genomes]
rs34042779	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs34088392	0.87[EUR][1000 genomes]
rs34173668	0.81[EUR][1000 genomes]
rs34234705	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34257602	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs34282385	0.87[EUR][1000 genomes]
rs34424197	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs34435758	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34486946	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34556569	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs34589937	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34646089	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs34796280	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34853395	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34933463	0.83[EUR][1000 genomes]
rs34958705	0.87[EUR][1000 genomes]
rs34997975	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35259011	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs35324423	0.83[EUR][1000 genomes]
rs35523559	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35607089	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35633657	0.83[EUR][1000 genomes]
rs35764401	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35984535	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs36004142	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs36056548	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs36126734	0.87[EUR][1000 genomes]
rs36175042	0.84[EUR][1000 genomes]
rs36185332	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4143844	0.81[EUR][1000 genomes]
rs4143845	0.87[EUR][1000 genomes]
rs62006964	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs62006969	0.84[EUR][1000 genomes]
rs62007448	0.82[EUR][1000 genomes]
rs62007764	0.98[EUR][1000 genomes]
rs62007768	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs62007791	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs62009074	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62009078	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62009082	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62009106	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62009109	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71411468	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71411469	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71411471	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs957348	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs978141	1.00[AFR][1000 genomes];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
rs35559361	VPS13C	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:62138800-62184200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:62139800-62185200	Weak transcription	NHLF	lung
3	chr15:62140000-62184800	Weak transcription	Right Ventricle	heart
4	chr15:62142000-62209400	Weak transcription	Colonic Mucosa	Colon
5	chr15:62142400-62253000	Weak transcription	Spleen	Spleen
6	chr15:62142600-62209200	Weak transcription	K562	blood
7	chr15:62143800-62235600	Weak transcription	Fetal Brain Male	brain
8	chr15:62144000-62194600	Weak transcription	Fetal Lung	lung
9	chr15:62144800-62184000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr15:62146800-62230000	Weak transcription	Pancreas	Pancrea
11	chr15:62147000-62184000	Weak transcription	Lung	lung
12	chr15:62147800-62184000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr15:62149000-62198000	Weak transcription	Fetal Kidney	kidney
14	chr15:62150000-62276200	Weak transcription	Psoas Muscle	Psoas
15	chr15:62150200-62184200	Weak transcription	Aorta	Aorta
16	chr15:62150200-62185400	Weak transcription	Fetal Heart	heart
17	chr15:62150800-62183800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr15:62153200-62185400	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr15:62153800-62185000	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr15:62154200-62198200	Weak transcription	NH-A	brain
21	chr15:62154400-62184200	Weak transcription	Fetal Intestine Small	intestine
22	chr15:62154600-62183800	Weak transcription	Brain Angular Gyrus	brain
23	chr15:62154800-62184200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr15:62155000-62184600	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr15:62161800-62184200	Weak transcription	Fetal Brain Female	brain
26	chr15:62162600-62195200	Weak transcription	Fetal Stomach	stomach
27	chr15:62163000-62184800	Weak transcription	Fetal Muscle Trunk	muscle
28	chr15:62163000-62198400	Weak transcription	Osteobl	bone
29	chr15:62163400-62184000	Weak transcription	Fetal Muscle Leg	muscle
30	chr15:62163600-62184800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr15:62163800-62184200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr15:62163800-62185400	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr15:62165400-62185000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr15:62165600-62185400	Weak transcription	Gastric	stomach
35	chr15:62165600-62198400	Weak transcription	Thymus	Thymus
36	chr15:62169000-62184200	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr15:62169200-62184000	Weak transcription	Rectal Smooth Muscle	rectum
38	chr15:62171800-62184000	Weak transcription	GM12878-XiMat	blood
39	chr15:62172000-62184600	Weak transcription	Stomach Mucosa	stomach
40	chr15:62172600-62184800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr15:62172600-62185200	Weak transcription	HepG2	liver
42	chr15:62173400-62198200	Weak transcription	Left Ventricle	heart
43	chr15:62177800-62184000	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr15:62178400-62183800	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr15:62178800-62184400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr15:62179000-62184000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr15:62179400-62184000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr15:62179400-62185200	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr15:62180000-62184400	Strong transcription	Primary B cells from cord blood	blood
50	chr15:62180200-62183600	Strong transcription	Rectal Mucosa Donor 31	rectum

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