Variant report

Variant	rs10166612
Chromosome Location	chr2:85804096-85804097
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZEB1	chr2:85803925-85806081	HepG2	liver:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:85764842..85767974-chr2:85803132..85805827,5	MCF-7	breast:
2	chr2:85786233..85788829-chr2:85802669..85804855,3	K562	blood:
3	chr2:85788298..85790199-chr2:85801505..85804429,2	MCF-7	breast:
4	chr2:85779865..85782682-chr2:85803471..85805138,2	MCF-7	breast:
5	chr2:85786233..85790202-chr2:85803177..85805521,3	K562	blood:
6	chr2:85764353..85768297-chr2:85801597..85805697,4	K562	blood:
7	chr2:85802926..85807956-chr2:85820760..85828546,8	K562	blood:
8	chr2:85764952..85767476-chr2:85803336..85806341,3	K562	blood:

No data

Variant related genes	Relation type
VAMP8	TF binding region
ENSG00000115486	Chromatin interaction
ENSG00000168890	Chromatin interaction
ENSG00000168894	Chromatin interaction
ENSG00000168906	Chromatin interaction
ENSG00000118640	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10167018	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10172793	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10174551	0.84[CEU][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10179904	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];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10187218	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10190585	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10196357	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10198001	0.84[CEU][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs10198761	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10202828	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10496316	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.89[ASN][1000 genomes]
rs12714142	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12714143	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.83[TSI][hapmap];0.82[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs12714144	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12714146	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12714147	0.87[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs12994163	0.84[CEU][hapmap]
rs13000511	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13387999	0.91[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs13394092	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs13406611	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13406935	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13408713	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13409377	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13421434	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]
rs13425821	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13426038	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];1.00[ASN][1000 genomes]
rs13429968	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13431159	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs13431962	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13432584	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17430670	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17508727	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17508809	1.00[CHB][hapmap]
rs17735885	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2121397	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];1.00[ASN][1000 genomes]
rs28398892	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28479378	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28564788	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28800839	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28810460	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34212016	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34214220	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34565621	0.90[AMR][1000 genomes]
rs34669893	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34824628	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35776719	0.93[ASN][1000 genomes]
rs55892665	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56359002	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62165899	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62165905	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62165907	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6727614	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7569073	1.00[CHB][hapmap]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10166612	VAMP5	Cis_1M	lymphoblastoid	RTeQTL
rs10166612	VAMP5	cis	lymphoblastoid	seeQTL

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85799400-85804200	Weak transcription	Primary T helper cells fromperipheralblood	blood
2	chr2:85799400-85804400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr2:85800200-85804800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:85802400-85804600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr2:85803000-85804400	Enhancers	Fetal Intestine Small	intestine
6	chr2:85803000-85804600	Enhancers	Placenta	Placenta
7	chr2:85803000-85804600	Enhancers	HUVEC	blood vessel
8	chr2:85803200-85804400	Enhancers	Fetal Intestine Large	intestine
9	chr2:85803200-85804400	Enhancers	Rectal Mucosa Donor 31	rectum
10	chr2:85803200-85804400	Flanking Active TSS	HepG2	liver
11	chr2:85803200-85804400	Enhancers	K562	blood
12	chr2:85803200-85804600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr2:85803200-85804600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr2:85803200-85804600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr2:85803400-85804200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr2:85803400-85804200	Enhancers	Duodenum Mucosa	Duodenum
17	chr2:85803400-85804200	Enhancers	Placenta Amnion	Placenta Amnion
18	chr2:85803400-85804200	Enhancers	Right Atrium	heart
19	chr2:85803400-85804200	Enhancers	A549	lung
20	chr2:85803400-85804400	Enhancers	Rectal Mucosa Donor 29	rectum
21	chr2:85803400-85804600	Enhancers	Adipose Nuclei	Adipose
22	chr2:85803400-85804600	Enhancers	Fetal Thymus	thymus
23	chr2:85803400-85804600	Enhancers	Stomach Mucosa	stomach
24	chr2:85803400-85804800	Enhancers	Fetal Muscle Leg	muscle
25	chr2:85803400-85805400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr2:85803600-85804600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr2:85803600-85804600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr2:85803600-85804600	Weak transcription	Fetal Lung	lung
29	chr2:85803600-85804600	Weak transcription	Left Ventricle	heart
30	chr2:85803600-85804600	Weak transcription	Lung	lung
31	chr2:85803600-85804600	Weak transcription	Psoas Muscle	Psoas
32	chr2:85803600-85804600	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr2:85803600-85804600	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr2:85803600-85804800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr2:85803600-85805800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr2:85803800-85804200	Enhancers	Primary hematopoietic stem cells short term culture	blood
37	chr2:85804000-85804200	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr2:85804000-85804200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr2:85804000-85804200	Enhancers	Monocytes-CD14+_RO01746	blood
40	chr2:85804000-85804400	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr2:85804000-85804400	Enhancers	Primary B cells from peripheral blood	blood
42	chr2:85804000-85804400	Enhancers	Primary T cells fromperipheralblood	blood
43	chr2:85804000-85804400	Enhancers	Primary hematopoietic stem cells	blood
44	chr2:85804000-85804400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
45	chr2:85804000-85804400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
46	chr2:85804000-85804400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr2:85804000-85804400	Enhancers	Liver	Liver
48	chr2:85804000-85804400	Enhancers	Pancreas	Pancrea
49	chr2:85804000-85804400	Flanking Active TSS	Hela-S3	cervix
50	chr2:85804000-85804400	Enhancers	HMEC	breast

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