Variant report

Variant	rs13421434
Chromosome Location	chr2:85807610-85807611
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF263	chr2:85807351-85807664	HEK293-T-REx	kidney:	n/a	chr2:85807434-85807443

No.	Distal block	Cell Line	Cell type
1	chr2:85787394..85789695-chr2:85806096..85808761,2	K562	blood:
2	chr2:85766314..85768748-chr2:85805954..85808781,2	MCF-7	breast:
3	chr2:85786998..85790131-chr2:85804287..85808110,8	MCF-7	breast:
4	chr2:85788344..85790079-chr2:85806686..85808273,2	K562	blood:
5	chr2:85802926..85807956-chr2:85820760..85828546,8	K562	blood:
6	chr2:85787502..85790371-chr2:85804560..85808548,6	MCF-7	breast:

Variant related genes	Relation type
VAMP5	TF binding region
ENSG00000168894	Chromatin interaction
ENSG00000168906	Chromatin interaction
ENSG00000118640	Chromatin interaction
ENSG00000168890	Chromatin interaction
ENSG00000115486	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10166612	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10167018	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10172793	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10174551	0.84[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs10179904	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10187218	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10190585	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10196357	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10198001	0.84[CEU][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10198761	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10202828	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10496316	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12714142	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12714143	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs12714144	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12714146	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12714147	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs12994163	0.84[CEU][hapmap]
rs13000511	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13387999	0.91[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs13394092	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs13406611	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13406935	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13408713	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13409377	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13425821	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13426038	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13429968	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13431159	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs13431962	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13432584	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17430670	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17508727	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17508809	1.00[CHB][hapmap]
rs17735885	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2121397	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28398892	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28479378	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28564788	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28800839	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28810460	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34212016	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34214220	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34565621	0.90[AMR][1000 genomes]
rs34669893	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34824628	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35776719	0.89[ASN][1000 genomes]
rs55892665	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56359002	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62165899	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62165905	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62165907	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6727614	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7569073	1.00[CHB][hapmap]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13421434	VAMP5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85804800-85807800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr2:85805000-85807800	Enhancers	Fetal Muscle Trunk	muscle
3	chr2:85805200-85807800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr2:85805800-85808200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr2:85805800-85808200	Enhancers	Esophagus	oesophagus
6	chr2:85805800-85810400	Weak transcription	Right Ventricle	heart
7	chr2:85805800-85810800	Weak transcription	Psoas Muscle	Psoas
8	chr2:85806000-85807800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr2:85806200-85807800	Enhancers	Primary T killer memory cells from peripheral blood	blood
10	chr2:85806200-85810800	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr2:85806200-85811000	Weak transcription	Colon Smooth Muscle	Colon
12	chr2:85806200-85811800	Weak transcription	A549	lung
13	chr2:85806400-85807800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr2:85806400-85807800	Enhancers	Right Atrium	heart
15	chr2:85806400-85810800	Weak transcription	Left Ventricle	heart
16	chr2:85806600-85807800	Enhancers	Primary B cells from cord blood	blood
17	chr2:85806600-85807800	Enhancers	Brain Hippocampus Middle	brain
18	chr2:85806600-85808200	Enhancers	Brain Anterior Caudate	brain
19	chr2:85806600-85808600	Weak transcription	Gastric	stomach
20	chr2:85806800-85807800	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr2:85806800-85807800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr2:85806800-85807800	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr2:85806800-85808200	Genic enhancers	Pancreas	Pancrea
24	chr2:85806800-85808200	Weak transcription	Rectal Smooth Muscle	rectum
25	chr2:85806800-85809000	Weak transcription	Hela-S3	cervix
26	chr2:85806800-85810400	Strong transcription	Sigmoid Colon	Sigmoid Colon
27	chr2:85806800-85810600	Weak transcription	HUVEC	blood vessel
28	chr2:85806800-85811000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr2:85807000-85807800	Enhancers	Primary neutrophils fromperipheralblood	blood
30	chr2:85807000-85807800	Enhancers	Primary T cells fromperipheralblood	blood
31	chr2:85807000-85807800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr2:85807000-85807800	Genic enhancers	Fetal Intestine Small	intestine
33	chr2:85807000-85807800	Enhancers	Thymus	Thymus
34	chr2:85807000-85807800	Enhancers	HMEC	breast
35	chr2:85807000-85808800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr2:85807000-85810000	Genic enhancers	Placenta	Placenta
37	chr2:85807000-85810600	Weak transcription	Fetal Kidney	kidney
38	chr2:85807000-85810800	Weak transcription	Brain Cingulate Gyrus	brain
39	chr2:85807000-85811000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr2:85807000-85811000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr2:85807000-85811400	Weak transcription	Small Intestine	intestine
42	chr2:85807200-85807800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr2:85807200-85808000	Enhancers	Primary monocytes fromperipheralblood	blood
44	chr2:85807200-85808800	Weak transcription	Colonic Mucosa	Colon
45	chr2:85807200-85810000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr2:85807200-85810400	Weak transcription	NHLF	lung
47	chr2:85807200-85810800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr2:85807200-85811000	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr2:85807400-85807800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr2:85807400-85807800	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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