Variant report

Variant	rs10913565
Chromosome Location	chr1:171706706-171706707
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:171704166..171707064-chr1:171814017..171815603,2	K562	blood:
2	chr1:171700285..171702286-chr1:171705548..171707475,2	K562	blood:
3	chr1:171703481..171707808-chr1:171708683..171714433,8	K562	blood:
4	chr1:171705072..171707837-chr1:171716105..171717838,2	K562	blood:
5	chr1:171702790..171705406-chr1:171705984..171707493,2	K562	blood:
6	chr1:171704087..171706245-chr1:171706489..171709352,2	MCF-7	breast:
7	chr1:171703871..171705878-chr1:171705948..171707617,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000117533	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1001373	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10489249	1.00[CEU][hapmap];0.84[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10489251	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1052676	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10903	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10913489	0.81[EUR][1000 genomes]
rs10913490	0.81[EUR][1000 genomes]
rs10913492	0.81[EUR][1000 genomes]
rs10913511	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10913514	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10913529	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10913578	0.83[JPT][hapmap]
rs10913582	1.00[CEU][hapmap];0.83[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10913587	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11576221	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs11577073	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11577197	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11577745	1.00[CEU][hapmap];0.83[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11578179	0.93[EUR][1000 genomes]
rs11578699	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11578723	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11579698	0.94[EUR][1000 genomes]
rs11580415	0.94[EUR][1000 genomes]
rs11580522	1.00[CEU][hapmap];0.83[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11583920	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11590680	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11590714	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11799420	0.81[EUR][1000 genomes]
rs11801846	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11803174	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11808099	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11811780	0.82[EUR][1000 genomes]
rs12119232	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12123727	0.81[EUR][1000 genomes]
rs12127026	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12128536	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12132221	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs15655	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16843251	0.83[JPT][hapmap]
rs17649050	1.00[CEU][hapmap];0.83[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17649068	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17649250	1.00[CEU][hapmap];0.83[JPT][hapmap]
rs2298914	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2421911	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3753539	0.83[JPT][hapmap]
rs3766653	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55670848	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58455759	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6656003	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6659874	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs6662720	1.00[CEU][hapmap]
rs6667559	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs6669263	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6670427	1.00[CEU][hapmap]
rs6678890	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6679354	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7528057	0.80[EUR][1000 genomes]
rs7536436	0.94[EUR][1000 genomes]
rs7536543	0.94[EUR][1000 genomes]
rs9661596	0.81[EUR][1000 genomes]
rs9662506	1.00[CEU][hapmap]
rs9662853	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv3512995	chr1:171329123-171994470	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	esv3512997	chr1:171329123-171994470	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	esv12447	chr1:171556291-171726822	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10913565	VAMP4	Cis_1M	lymphoblastoid	RTeQTL
rs10913565	VAMP4	cis	Temporal Cortex	GTEx
rs10913565	VAMP4	cis	Brain Pons	GTEx
rs10913565	VAMP4	cis	Frontal Cortex	GTEx
rs10913565	VAMP4	cis	multi-tissue	Pritchard

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171665600-171708800	Weak transcription	Brain Angular Gyrus	brain
2	chr1:171668800-171708200	Weak transcription	Small Intestine	intestine
3	chr1:171686600-171710400	Weak transcription	Esophagus	oesophagus
4	chr1:171686600-171710400	Weak transcription	Gastric	stomach
5	chr1:171687600-171708000	Weak transcription	K562	blood
6	chr1:171692400-171708400	Weak transcription	Brain Substantia Nigra	brain
7	chr1:171692400-171710400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:171692400-171710400	Weak transcription	Lung	lung
9	chr1:171692600-171708400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr1:171692600-171709800	Weak transcription	Stomach Mucosa	stomach
11	chr1:171692600-171710200	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr1:171693200-171709800	Weak transcription	Fetal Kidney	kidney
13	chr1:171694800-171709000	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr1:171695000-171710400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:171695600-171708400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr1:171696000-171710200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr1:171696200-171710400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr1:171696400-171709800	Weak transcription	Psoas Muscle	Psoas
19	chr1:171697200-171710000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr1:171697600-171708200	Weak transcription	Spleen	Spleen
21	chr1:171697600-171708400	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr1:171699400-171708200	Weak transcription	Hela-S3	cervix
23	chr1:171699800-171709600	Weak transcription	Rectal Smooth Muscle	rectum
24	chr1:171701200-171707400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr1:171701600-171707800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr1:171702200-171707800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr1:171702400-171707600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr1:171702400-171707600	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr1:171702400-171708000	Strong transcription	Primary B cells from peripheral blood	blood
30	chr1:171702600-171707400	Strong transcription	Liver	Liver
31	chr1:171702600-171707800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr1:171702800-171707600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr1:171702800-171707600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr1:171702800-171708000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr1:171703000-171709600	Weak transcription	Colonic Mucosa	Colon
36	chr1:171703200-171707800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr1:171703400-171707600	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr1:171703600-171707400	Strong transcription	NHDF-Ad	bronchial
39	chr1:171703600-171708000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr1:171704000-171707000	Strong transcription	Placenta	Placenta
41	chr1:171704000-171708000	Strong transcription	Primary B cells from cord blood	blood
42	chr1:171704200-171706800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr1:171704200-171707400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr1:171704200-171707600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr1:171704200-171707600	Strong transcription	Primary hematopoietic stem cells	blood
46	chr1:171704200-171708000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr1:171704400-171707800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr1:171704400-171708000	Strong transcription	Osteobl	bone
49	chr1:171704600-171707400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr1:171704600-171707400	Strong transcription	Primary neutrophils fromperipheralblood	blood

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