Variant report

Variant	rs6738645
Chromosome Location	chr2:85783128-85783129
allele	G/T
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:7)
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	POLR2A	chr2:85782937-85783388	HepG2	liver:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:85781595..85783590-chr2:85822310..85824885,2	MCF-7	breast:
2	chr2:85635544..85709381-chr2:85757395..85791508,633	K562	blood:
3	chr2:85609654..85691056-chr2:85759187..85790499,656	K562	blood:
4	chr2:85782911..85784755-chr2:85838569..85840663,2	MCF-7	breast:
5	chr2:85595072..85597538-chr2:85782216..85784797,2	K562	blood:
6	chr2:85782564..85785342-chr2:85825387..85826998,2	MCF-7	breast:
7	chr2:85646535..85649552-chr2:85782330..85785988,4	MCF-7	breast:

No data

Variant related genes	Relation type
GGCX	TF binding region
ENSG00000273196	Chromatin interaction
ENSG00000244399	Chromatin interaction
ENSG00000115459	Chromatin interaction
ENSG00000042493	Chromatin interaction
ENSG00000207207	Chromatin interaction
ENSG00000199936	Chromatin interaction
ENSG00000168894	Chromatin interaction
ENSG00000168887	Chromatin interaction
ENSG00000152292	Chromatin interaction
ENSG00000252293	Chromatin interaction
ENSG00000168883	Chromatin interaction
ENSG00000242095	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1009	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs1010	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1011	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10172544	0.99[ASN][1000 genomes]
rs10175792	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10176176	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10179195	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10187424	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10198569	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10206961	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1058588	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1078004	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11891260	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12473819	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12714145	0.99[ASN][1000 genomes]
rs13394343	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1348818	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs1446669	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs1561198	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1562323	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17026396	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1972297	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2028898	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs2028900	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2043675	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs2044474	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2166529	0.92[CEU][hapmap];0.81[CHB][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2232748	0.81[JPT][hapmap]
rs2289972	0.86[CHB][hapmap]
rs2366639	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2592551	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs2886722	0.81[CHB][hapmap]
rs35215812	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3731827	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3731828	0.86[CHB][hapmap]
rs3755014	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3755015	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3770098	0.83[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]
rs55971080	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59877521	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6547620	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6547621	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6547624	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6547629	0.80[JPT][hapmap]
rs6705839	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6705971	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6714157	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6714709	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6721924	0.91[ASN][1000 genomes]
rs6731005	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6733550	0.80[JPT][hapmap]
rs6733913	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6735152	0.93[ASN][1000 genomes]
rs6738009	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6739015	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6743030	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6750832	0.86[ASN][1000 genomes]
rs6750847	0.94[ASN][1000 genomes]
rs6757263	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]
rs67988001	0.80[ASN][1000 genomes]
rs699664	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs7568458	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7579147	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs7591175	0.93[CEU][hapmap];0.82[CHB][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7593969	0.86[CHB][hapmap]
rs7605975	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs762684	0.86[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs6738645	VAMP8	cis	multi-tissue	Pritchard
rs6738645	GGCX	cis	multi-tissue	Pritchard
rs6738645	VAMP8	cis	uninvolved skin	skin_eQTL
rs6738645	GGCX	cis	Artery Aorta	GTEx
rs6738645	VAMP8	Cis_1M	lymphoblastoid	RTeQTL
rs6738645	VAMP8	cis	lesional skin	skin_eQTL
rs6738645	GGCX	cis	Whole Blood	GTEx
rs6738645	VAMP8	cis	Esophagus Mucosa	GTEx
rs6738645	GGCX	cis	Artery Tibial	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85768400-85786600	Strong transcription	Fetal Muscle Trunk	muscle
2	chr2:85768600-85786200	Strong transcription	Fetal Thymus	thymus
3	chr2:85769400-85786600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:85769400-85786600	Strong transcription	Brain Germinal Matrix	brain
5	chr2:85769400-85787800	Weak transcription	Right Atrium	heart
6	chr2:85769800-85786400	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr2:85769800-85787000	Strong transcription	Fetal Stomach	stomach
8	chr2:85769800-85788000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr2:85770000-85783400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr2:85770200-85787800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr2:85770400-85786200	Strong transcription	Fetal Intestine Large	intestine
12	chr2:85770400-85786400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr2:85770600-85786400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr2:85770600-85786600	Strong transcription	Fetal Brain Female	brain
15	chr2:85771000-85786400	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr2:85771800-85786200	Strong transcription	Fetal Intestine Small	intestine
17	chr2:85772000-85786600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr2:85773400-85786200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr2:85774600-85786200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr2:85775600-85786600	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr2:85775800-85783400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr2:85776200-85785000	Strong transcription	HepG2	liver
23	chr2:85776200-85786000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr2:85776200-85786400	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr2:85776200-85786400	Strong transcription	Duodenum Mucosa	Duodenum
26	chr2:85776400-85783200	Strong transcription	Colon Smooth Muscle	Colon
27	chr2:85776600-85784000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr2:85776600-85787000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr2:85776800-85784200	Strong transcription	Stomach Smooth Muscle	stomach
30	chr2:85776800-85785000	Strong transcription	Dnd41	blood
31	chr2:85776800-85786200	Strong transcription	Primary T cells from cord blood	blood
32	chr2:85777000-85783400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr2:85777000-85783400	Strong transcription	Colonic Mucosa	Colon
34	chr2:85777000-85784000	Strong transcription	Brain Cingulate Gyrus	brain
35	chr2:85777000-85784000	Strong transcription	Left Ventricle	heart
36	chr2:85777000-85784400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr2:85777000-85785800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr2:85777000-85786200	Strong transcription	Sigmoid Colon	Sigmoid Colon
39	chr2:85777000-85786400	Strong transcription	H9 Cell Line	embryonic stem cell
40	chr2:85777000-85786400	Strong transcription	Lung	lung
41	chr2:85777000-85787200	Strong transcription	NHEK	skin
42	chr2:85777200-85784200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr2:85777200-85784200	Strong transcription	GM12878-XiMat	blood
44	chr2:85777200-85785800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
45	chr2:85777200-85786400	Strong transcription	Rectal Smooth Muscle	rectum
46	chr2:85777200-85786600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr2:85777400-85783400	Strong transcription	Gastric	stomach
48	chr2:85777400-85783600	Strong transcription	Fetal Lung	lung
49	chr2:85777400-85783600	Strong transcription	HMEC	breast
50	chr2:85777400-85786400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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