Variant report

Variant	rs6757263
Chromosome Location	chr2:85803542-85803543
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFK	chr2:85803407-85803551	HepG2	liver:	n/a	n/a
2	MYBL2	chr2:85803062-85803736	HepG2	liver:	n/a	n/a
3	HDAC2	chr2:85803263-85803578	HepG2	liver:	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	KAP1	chr2:85803421-85803601	HEK293	kidney:	n/a	n/a
8	ZNF384	chr2:85803478-85803846	K562	blood:	n/a	n/a
9	RXRA	chr2:85803315-85803651	HepG2	liver:	n/a	n/a
10	CUX1	chr2:85803418-85803677	K562	blood:	n/a	n/a
11	NFIC	chr2:85803322-85803683	HepG2	liver:	n/a	n/a
12	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	chr2:85779865..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
ENSG00000168906	Chromatin interaction
ENSG00000118640	Chromatin interaction
ENSG00000168890	Chromatin interaction
ENSG00000168894	Chromatin interaction
ENSG00000115486	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1009	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]
rs1010	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1011	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10172544	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10175792	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10176176	0.86[ASN][1000 genomes]
rs10179195	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs10187424	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10198569	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10206961	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs1058588	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1078004	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11891260	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12473819	0.87[ASN][1000 genomes]
rs12714145	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13394343	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13411109	0.83[AMR][1000 genomes]
rs1348818	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1446669	0.82[CHB][hapmap];0.81[CHD][hapmap];0.81[JPT][hapmap]
rs1561198	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1562323	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17026396	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1972297	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2028898	0.86[CHB][hapmap];0.80[CHD][hapmap];0.81[JPT][hapmap]
rs2028900	0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs2043675	0.86[CHB][hapmap];0.81[CHD][hapmap];0.81[JPT][hapmap]
rs2044474	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2166529	0.81[CHB][hapmap]
rs2289972	0.86[CHB][hapmap]
rs2366639	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2592551	0.86[CHB][hapmap];0.83[CHD][hapmap];0.81[JPT][hapmap]
rs2886722	0.89[CEU][hapmap];0.81[CHB][hapmap]
rs35215812	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35565292	0.87[AMR][1000 genomes]
rs3731827	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3731828	0.86[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap]
rs3755014	0.86[ASN][1000 genomes]
rs3755015	0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs3770098	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55971080	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59877521	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6547620	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6547621	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6547624	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6705839	0.82[ASN][1000 genomes]
rs6705971	0.82[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs6714157	0.85[ASN][1000 genomes]
rs6714709	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6721924	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6731005	0.84[ASN][1000 genomes]
rs6733913	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6735152	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6738645	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6739015	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6743030	0.86[ASN][1000 genomes]
rs6750847	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs699664	0.86[CHB][hapmap];0.83[CHD][hapmap];0.81[JPT][hapmap]
rs7568458	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7579147	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs7591175	0.81[CHB][hapmap]
rs7593969	0.86[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap]
rs7605975	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs762684	0.86[CHB][hapmap];0.81[JPT][hapmap]

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs6757263	LOC388969	cis	multi-tissue	Pritchard
rs6757263	GGCX	cis	Artery Tibial	GTEx
rs6757263	VAMP8	cis	lymphoblastoid	seeQTL
rs6757263	VAMP8	cis	Esophagus Mucosa	GTEx
rs6757263	MAT2A	cis	cerebellum	SCAN
rs6757263	GGCX	cis	multi-tissue	Pritchard
rs6757263	VAMP8	cis	multi-tissue	Pritchard
rs6757263	GGCX	cis	Whole Blood	GTEx
rs6757263	RNF103	cis	parietal	SCAN
rs6757263	VAMP8	cis	uninvolved skin	skin_eQTL
rs6757263	GGCX	cis	Artery Aorta	GTEx
rs6757263	GGCX	cis	Nerve Tibial	GTEx
rs6757263	GGCX	cis	cerebellum	SCAN
rs6757263	GGCX	cis	parietal	SCAN
rs6757263	VAMP8	cis	parietal	SCAN
rs6757263	VAMP8	cis	lesional skin	skin_eQTL
rs6757263	GGCX	cis	Thyroid	GTEx

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85789400-85804000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr2:85799400-85804200	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr2:85799400-85804400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr2:85800200-85804800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:85802400-85804600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr2:85803000-85804400	Enhancers	Fetal Intestine Small	intestine
7	chr2:85803000-85804600	Enhancers	Placenta	Placenta
8	chr2:85803000-85804600	Enhancers	HUVEC	blood vessel
9	chr2:85803200-85803600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr2:85803200-85803600	Enhancers	Fetal Lung	lung
11	chr2:85803200-85803800	Flanking Active TSS	Hela-S3	cervix
12	chr2:85803200-85804400	Enhancers	Fetal Intestine Large	intestine
13	chr2:85803200-85804400	Enhancers	Rectal Mucosa Donor 31	rectum
14	chr2:85803200-85804400	Flanking Active TSS	HepG2	liver
15	chr2:85803200-85804400	Enhancers	K562	blood
16	chr2:85803200-85804600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr2:85803200-85804600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr2:85803200-85804600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr2:85803400-85803600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr2:85803400-85803600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr2:85803400-85803600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
22	chr2:85803400-85803600	Enhancers	Fetal Kidney	kidney
23	chr2:85803400-85803600	Enhancers	Left Ventricle	heart
24	chr2:85803400-85803600	Enhancers	Lung	lung
25	chr2:85803400-85803600	Enhancers	Psoas Muscle	Psoas
26	chr2:85803400-85803600	Enhancers	Sigmoid Colon	Sigmoid Colon
27	chr2:85803400-85803600	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr2:85803400-85804000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr2:85803400-85804000	Weak transcription	Liver	Liver
30	chr2:85803400-85804200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr2:85803400-85804200	Enhancers	Duodenum Mucosa	Duodenum
32	chr2:85803400-85804200	Enhancers	Placenta Amnion	Placenta Amnion
33	chr2:85803400-85804200	Enhancers	Right Atrium	heart
34	chr2:85803400-85804200	Enhancers	A549	lung
35	chr2:85803400-85804400	Enhancers	Rectal Mucosa Donor 29	rectum
36	chr2:85803400-85804600	Enhancers	Adipose Nuclei	Adipose
37	chr2:85803400-85804600	Enhancers	Fetal Thymus	thymus
38	chr2:85803400-85804600	Enhancers	Stomach Mucosa	stomach
39	chr2:85803400-85804800	Enhancers	Fetal Muscle Leg	muscle
40	chr2:85803400-85805400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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