Variant report

Variant	rs13426038
Chromosome Location	chr2:85803398-85803399
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYBL2	chr2:85803062-85803736	HepG2	liver:	n/a	n/a
2	HDAC2	chr2:85803263-85803578	HepG2	liver:	n/a	n/a
3	RCOR1	chr2:85803366-85803524	K562	blood:	n/a	n/a
4	MYBL2	chr2:85802955-85803720	HepG2	liver:	n/a	n/a
5	EP300	chr2:85803116-85803746	HepG2	liver:	n/a	n/a
6	NFIC	chr2:85803084-85803735	HepG2	liver:	n/a	n/a
7	RXRA	chr2:85803315-85803651	HepG2	liver:	n/a	n/a
8	NFIC	chr2:85803322-85803683	HepG2	liver:	n/a	n/a
9	SP1	chr2:85803163-85803803	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	chr2:85792954..85795651-chr2:85800835..85803486,2	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
ENSG00000168890	Chromatin interaction
ENSG00000266536	Chromatin interaction
ENSG00000168894	Chromatin interaction
ENSG00000115486	Chromatin interaction
ENSG00000118640	Chromatin interaction
ENSG00000168906	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[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]
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]
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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13426038	VAMP5	cis	lymphoblastoid	seeQTL

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85789400-85803400	Weak transcription	Adipose Nuclei	Adipose
2	chr2:85789400-85803400	Weak transcription	Right Atrium	heart
3	chr2:85789400-85804000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr2:85799400-85804200	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr2:85799400-85804400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr2:85800200-85804800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:85802400-85804600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr2:85803000-85804400	Enhancers	Fetal Intestine Small	intestine
9	chr2:85803000-85804600	Enhancers	Placenta	Placenta
10	chr2:85803000-85804600	Enhancers	HUVEC	blood vessel
11	chr2:85803200-85803400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr2:85803200-85803400	Enhancers	Liver	Liver
13	chr2:85803200-85803600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr2:85803200-85803600	Enhancers	Fetal Lung	lung
15	chr2:85803200-85803800	Flanking Active TSS	Hela-S3	cervix
16	chr2:85803200-85804400	Enhancers	Fetal Intestine Large	intestine
17	chr2:85803200-85804400	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr2:85803200-85804400	Flanking Active TSS	HepG2	liver
19	chr2:85803200-85804400	Enhancers	K562	blood
20	chr2:85803200-85804600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr2:85803200-85804600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr2:85803200-85804600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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