Variant report

Variant	rs7593969
Chromosome Location	chr2:85809670-85809671
allele	C/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:5)
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	chr2:85809579-85810134	HL-60	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:85764082..85769632-chr2:85809376..85814783,9	K562	blood:
2	chr2:85764767..85768368-chr2:85809376..85813309,5	K562	blood:
3	chr2:85780429..85781950-chr2:85809596..85811183,2	MCF-7	breast:
4	chr2:85764932..85768576-chr2:85809550..85811376,5	MCF-7	breast:
5	chr2:85788681..85792834-chr2:85809475..85813834,4	MCF-7	breast:

No data

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

Extended variants
information (count: 58 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1009	0.86[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap]
rs1010	0.85[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap]
rs1011	0.80[ASN][1000 genomes]
rs10179195	0.95[CHB][hapmap]
rs10187424	0.86[CHB][hapmap];0.83[CHD][hapmap]
rs10198569	0.86[CHB][hapmap];0.85[CHD][hapmap]
rs10206961	0.86[CHB][hapmap];0.80[CHD][hapmap]
rs1058588	0.86[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs1078004	0.86[CHB][hapmap]
rs11126995	0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11311	0.90[ASN][1000 genomes]
rs11895341	0.86[ASN][1000 genomes]
rs11895399	0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs11895401	0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12615553	0.90[ASN][1000 genomes]
rs1348818	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs14242	0.84[JPT][hapmap]
rs1446669	0.93[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.86[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs1561198	0.86[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs1562322	0.84[JPT][hapmap]
rs1562323	0.80[ASN][1000 genomes]
rs17026396	0.90[CHB][hapmap];0.80[CHD][hapmap]
rs1972297	0.80[ASN][1000 genomes]
rs2028898	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2028900	0.86[CHB][hapmap];0.80[CHD][hapmap]
rs2043675	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2044474	0.90[CHB][hapmap]
rs2289972	0.93[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2366639	0.80[ASN][1000 genomes]
rs2592551	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3731827	0.80[ASN][1000 genomes]
rs3731828	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3755008	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3755011	0.84[JPT][hapmap]
rs3755015	0.90[CHB][hapmap]
rs3770098	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs55692129	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56819945	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58307667	0.82[ASN][1000 genomes]
rs58768785	0.90[ASN][1000 genomes]
rs60012532	0.83[ASN][1000 genomes]
rs60788310	0.89[ASN][1000 genomes]
rs6547621	0.86[CHB][hapmap]
rs6547622	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6547623	0.90[ASN][1000 genomes]
rs6705971	0.90[CHB][hapmap]
rs6722691	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6731700	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6738645	0.86[CHB][hapmap]
rs6757263	0.86[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap]
rs67988001	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs699664	1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs72643495	0.83[ASN][1000 genomes]
rs73943244	0.92[ASN][1000 genomes]
rs7568458	0.86[CHB][hapmap]
rs7579147	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7608074	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs762684	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs7593969	VAMP8	cis	parietal	SCAN
rs7593969	GGCX	cis	cerebellum	SCAN
rs7593969	VAMP8	cis	Esophagus Mucosa	GTEx
rs7593969	VAMP8	Cis_1M	lymphoblastoid	RTeQTL
rs7593969	RNF103	cis	parietal	SCAN
rs7593969	VAMP8	cis	multi-tissue	Pritchard
rs7593969	GGCX	cis	parietal	SCAN
rs7593969	RNF181	cis	parietal	SCAN
rs7593969	VAMP8	cis	lymphoblastoid	seeQTL
rs7593969	MAT2A	cis	cerebellum	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85805800-85810400	Weak transcription	Right Ventricle	heart
2	chr2:85805800-85810800	Weak transcription	Psoas Muscle	Psoas
3	chr2:85806200-85810800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr2:85806200-85811000	Weak transcription	Colon Smooth Muscle	Colon
5	chr2:85806200-85811800	Weak transcription	A549	lung
6	chr2:85806400-85810800	Weak transcription	Left Ventricle	heart
7	chr2:85806800-85810400	Strong transcription	Sigmoid Colon	Sigmoid Colon
8	chr2:85806800-85810600	Weak transcription	HUVEC	blood vessel
9	chr2:85806800-85811000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr2:85807000-85810000	Genic enhancers	Placenta	Placenta
11	chr2:85807000-85810600	Weak transcription	Fetal Kidney	kidney
12	chr2:85807000-85810800	Weak transcription	Brain Cingulate Gyrus	brain
13	chr2:85807000-85811000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr2:85807000-85811000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr2:85807000-85811400	Weak transcription	Small Intestine	intestine
16	chr2:85807200-85810000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr2:85807200-85810400	Weak transcription	NHLF	lung
18	chr2:85807200-85810800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr2:85807200-85811000	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr2:85807400-85810000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr2:85807400-85810600	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr2:85807400-85810800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr2:85807400-85810800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr2:85807400-85810800	Weak transcription	Stomach Smooth Muscle	stomach
25	chr2:85807400-85810800	Weak transcription	HSMMtube	muscle
26	chr2:85807400-85811200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr2:85807600-85810000	Strong transcription	Primary B cells from peripheral blood	blood
28	chr2:85807600-85810400	Strong transcription	Primary T cells from cord blood	blood
29	chr2:85807600-85810400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr2:85807600-85810600	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr2:85807600-85810800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr2:85807600-85810800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr2:85807600-85810800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr2:85807600-85810800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr2:85807600-85810800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr2:85807600-85810800	Weak transcription	Fetal Muscle Leg	muscle
37	chr2:85807600-85810800	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr2:85807600-85810800	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr2:85807600-85810800	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr2:85807600-85810800	Weak transcription	HSMM	muscle
41	chr2:85807600-85811000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr2:85807600-85811000	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr2:85807600-85811000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr2:85807600-85811000	Weak transcription	Fetal Lung	lung
45	chr2:85807600-85811000	Weak transcription	Stomach Mucosa	stomach
46	chr2:85807600-85811200	Strong transcription	NHEK	skin
47	chr2:85807600-85811600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr2:85807600-85812400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr2:85807800-85809800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr2:85807800-85809800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links