Variant report

Variant	rs6643
Chromosome Location	chr2:85824251-85824252
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:85802926..85807956-chr2:85820760..85828546,8	K562	blood:
2	chr2:85645665..85648237-chr2:85822312..85824673,3	MCF-7	breast:
3	chr2:85785429..85790468-chr2:85820934..85826927,9	MCF-7	breast:
4	chr2:85764454..85770994-chr2:85819148..85831427,14	K562	blood:
5	chr2:85777446..85780419-chr2:85822995..85825315,2	MCF-7	breast:
6	chr2:85781595..85783590-chr2:85822310..85824885,2	MCF-7	breast:
7	chr2:85788313..85790312-chr2:85822619..85824449,2	K562	blood:
8	chr2:85765572..85767946-chr2:85820164..85824365,5	MCF-7	breast:
9	chr2:85764018..85768553-chr2:85822883..85829718,12	MCF-7	breast:
10	chr2:85765237..85769549-chr2:85821409..85826975,10	K562	blood:

No data

Variant related genes	Relation type
ENSG00000152292	Chromatin interaction
ENSG00000115486	Chromatin interaction
ENSG00000168906	Chromatin interaction
ENSG00000118640	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10180770	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10182351	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs10190428	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10191726	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10302	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1044158	0.81[CHB][hapmap];0.84[CHD][hapmap]
rs1124836	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13383605	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13414982	1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[TSI][hapmap]
rs13418207	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs14242	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1446669	0.84[JPT][hapmap]
rs1562322	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1992151	0.81[EUR][1000 genomes]
rs2028898	0.84[JPT][hapmap]
rs2043675	0.84[JPT][hapmap]
rs2118176	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2232745	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2232747	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2232748	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs2232750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2304564	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2592551	0.84[JPT][hapmap]
rs3024831	1.00[CEU][hapmap];0.90[GIH][hapmap]
rs3198089	1.00[CEU][hapmap];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3755009	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3755010	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3755011	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3821020	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs3827550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6547629	0.81[CHB][hapmap];0.81[CHD][hapmap];0.81[JPT][hapmap]
rs6733550	0.80[CHB][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap]
rs6743051	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs699664	0.84[JPT][hapmap]
rs762684	0.84[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv992753	chr2:85822210-85825244	Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6643	VAMP8	cis	lymphoblastoid	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85823200-85824400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:85823200-85825000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr2:85823200-85829200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr2:85823600-85824400	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr2:85823600-85824400	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
6	chr2:85823600-85824600	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
7	chr2:85823600-85824600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr2:85823600-85824800	Enhancers	Fetal Heart	heart
9	chr2:85823600-85825000	Genic enhancers	Gastric	stomach
10	chr2:85823600-85829000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr2:85823800-85824400	Transcr. at gene 5' and 3'	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr2:85823800-85824400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr2:85823800-85824400	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr2:85823800-85824400	Genic enhancers	Primary monocytes fromperipheralblood	blood
15	chr2:85823800-85824400	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr2:85823800-85824400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr2:85823800-85824400	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr2:85823800-85824400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr2:85823800-85824400	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr2:85823800-85824400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr2:85823800-85824400	Genic enhancers	Esophagus	oesophagus
22	chr2:85823800-85824400	Genic enhancers	Fetal Muscle Trunk	muscle
23	chr2:85823800-85824400	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 29	rectum
24	chr2:85823800-85824400	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
25	chr2:85823800-85824400	Transcr. at gene 5' and 3'	HSMMtube	muscle
26	chr2:85823800-85824400	Enhancers	HUVEC	blood vessel
27	chr2:85823800-85824600	Genic enhancers	Brain Angular Gyrus	brain
28	chr2:85823800-85824600	Genic enhancers	Brain Cingulate Gyrus	brain
29	chr2:85823800-85824600	Enhancers	Fetal Brain Male	brain
30	chr2:85823800-85824600	Genic enhancers	Placenta	Placenta
31	chr2:85823800-85824600	Genic enhancers	Placenta Amnion	Placenta Amnion
32	chr2:85823800-85824600	Transcr. at gene 5' and 3'	Dnd41	blood
33	chr2:85823800-85824800	Genic enhancers	Spleen	Spleen
34	chr2:85823800-85825000	Genic enhancers	Primary B cells from cord blood	blood
35	chr2:85823800-85825000	Genic enhancers	Primary T cells fromperipheralblood	blood
36	chr2:85823800-85826000	Transcr. at gene 5' and 3'	HepG2	liver
37	chr2:85823800-85828800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr2:85824000-85824400	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr2:85824000-85824400	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr2:85824000-85824400	Genic enhancers	Primary neutrophils fromperipheralblood	blood
41	chr2:85824000-85824400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr2:85824000-85824400	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
43	chr2:85824000-85824400	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
44	chr2:85824000-85824400	Genic enhancers	Brain Inferior Temporal Lobe	brain
45	chr2:85824000-85824400	Genic enhancers	Colonic Mucosa	Colon
46	chr2:85824000-85824400	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 31	rectum
47	chr2:85824000-85824400	Transcr. at gene 5' and 3'	Rectal Smooth Muscle	rectum
48	chr2:85824000-85824400	Transcr. at gene 5' and 3'	NHLF	lung
49	chr2:85824000-85824600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr2:85824000-85824600	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood

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