Variant report

Variant	rs3770098
Chromosome Location	chr2:85805367-85805368
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:85764842..85767974-chr2:85803132..85805827,5	MCF-7	breast:
2	chr2:85786998..85790131-chr2:85804287..85808110,8	MCF-7	breast:
3	chr2:85804681..85806914-chr2:85828981..85831310,3	K562	blood:
4	chr2:85786233..85790202-chr2:85803177..85805521,3	K562	blood:
5	chr19:34012225..34012843-chr2:85804512..85805471,2	Hela-S3	cervix:
6	chr2:85647853..85649461-chr2:85804222..85806798,2	K562	blood:
7	chr2:85764353..85768297-chr2:85801597..85805697,4	K562	blood:
8	chr2:85802926..85807956-chr2:85820760..85828546,8	K562	blood:
9	chr2:85787502..85790371-chr2:85804560..85808548,6	MCF-7	breast:
10	chr2:85764952..85767476-chr2:85803336..85806341,3	K562	blood:
11	chr2:85804757..85805378-chr2:122406950..122407883,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
ENSG00000115486	Chromatin interaction
ENSG00000152292	Chromatin interaction
ENSG00000124299	Chromatin interaction
ENSG00000074054	Chromatin interaction
ENSG00000168906	Chromatin interaction
ENSG00000168883	Chromatin interaction
ENSG00000168894	Chromatin interaction
ENSG00000118640	Chromatin interaction
ENSG00000236859	Chromatin interaction
ENSG00000168890	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 12 )

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

rs_ID	r²[population]
rs1009	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1010	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[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];0.90[ASN][1000 genomes]
rs10175792	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10176176	0.86[ASN][1000 genomes]
rs10179195	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs10187424	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10198569	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10206961	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs1058588	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1078004	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11891260	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12473819	0.86[ASN][1000 genomes]
rs12714145	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13394343	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13411109	0.83[AMR][1000 genomes]
rs1348818	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1446669	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs1561198	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1562323	0.92[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];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1972297	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2028898	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs2028900	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2043675	0.86[CHB][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];0.85[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];0.81[JPT][hapmap]
rs2886722	0.89[CEU][hapmap];0.81[CHB][hapmap]
rs35215812	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35565292	0.87[AMR][1000 genomes]
rs3731827	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3731828	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs3755014	0.86[ASN][1000 genomes]
rs3755015	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs55971080	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59877521	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6547620	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6547621	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6547624	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6705839	0.84[ASN][1000 genomes]
rs6705971	0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs6714157	0.87[ASN][1000 genomes]
rs6714709	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6721924	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6731005	0.86[ASN][1000 genomes]
rs6733913	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6735152	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6738645	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]
rs6739015	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6743030	0.85[ASN][1000 genomes]
rs6750847	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6757263	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]
rs699664	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs7568458	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7579147	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs7591175	0.82[CHB][hapmap]
rs7593969	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs7605975	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs762684	0.86[CHB][hapmap];0.82[JPT][hapmap]

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs3770098	VAMP8	cis	uninvolved skin	skin_eQTL
rs3770098	GGCX	cis	Artery Tibial	GTEx
rs3770098	LOC388969	cis	multi-tissue	Pritchard
rs3770098	VAMP8	cis	multi-tissue	Pritchard
rs3770098	GGCX	cis	Nerve Tibial	GTEx
rs3770098	GGCX	cis	Artery Aorta	GTEx
rs3770098	VAMP8	Cis_1M	lymphoblastoid	RTeQTL
rs3770098	GGCX	Cis_1M	lymphoblastoid	RTeQTL
rs3770098	VAMP8	cis	lesional skin	skin_eQTL
rs3770098	GGCX	cis	Thyroid	GTEx
rs3770098	GGCX	cis	Whole Blood	GTEx
rs3770098	VAMP8	cis	Esophagus Mucosa	GTEx

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85803400-85805400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr2:85803600-85805800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr2:85804000-85806800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr2:85804200-85805600	Active TSS	A549	lung
5	chr2:85804200-85806000	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr2:85804200-85807400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr2:85804200-85807600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
8	chr2:85804400-85805400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr2:85804400-85805600	Active TSS	Fetal Intestine Large	intestine
10	chr2:85804400-85805600	Active TSS	Pancreas	Pancrea
11	chr2:85804400-85805600	Active TSS	Rectal Mucosa Donor 31	rectum
12	chr2:85804400-85805600	Active TSS	GM12878-XiMat	blood
13	chr2:85804400-85805800	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr2:85804400-85806000	Flanking Active TSS	Liver	Liver
15	chr2:85804400-85806400	Flanking Active TSS	Primary B cells from peripheral blood	blood
16	chr2:85804400-85806600	Flanking Active TSS	Primary B cells from cord blood	blood
17	chr2:85804400-85806600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
18	chr2:85804400-85806600	Flanking Active TSS	HSMM	muscle
19	chr2:85804400-85806600	Flanking Active TSS	HSMMtube	muscle
20	chr2:85804400-85806800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
21	chr2:85804400-85807000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
22	chr2:85804400-85807000	Flanking Active TSS	Thymus	Thymus
23	chr2:85804400-85807400	Flanking Active TSS	Primary hematopoietic stem cells	blood
24	chr2:85804600-85805400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
25	chr2:85804600-85805400	Active TSS	H9 Cell Line	embryonic stem cell
26	chr2:85804600-85805400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr2:85804600-85805400	Active TSS	iPS-18 Cell Line	embryonic stem cell
28	chr2:85804600-85805400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr2:85804600-85805400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
30	chr2:85804600-85805400	Active TSS	Colonic Mucosa	Colon
31	chr2:85804600-85805400	Active TSS	Placenta Amnion	Placenta Amnion
32	chr2:85804600-85805400	Transcr. at gene 5' and 3'	Right Atrium	heart
33	chr2:85804600-85805400	Active TSS	K562	blood
34	chr2:85804600-85805600	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
35	chr2:85804600-85805600	Active TSS	Primary T helper cells PMA-I stimulated	--
36	chr2:85804600-85805600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
37	chr2:85804600-85805600	Active TSS	Brain Hippocampus Middle	brain
38	chr2:85804600-85805600	Active TSS	Esophagus	oesophagus
39	chr2:85804600-85805600	Active TSS	Fetal Intestine Small	intestine
40	chr2:85804600-85805600	Active TSS	Rectal Mucosa Donor 29	rectum
41	chr2:85804600-85805600	Active TSS	Sigmoid Colon	Sigmoid Colon
42	chr2:85804600-85805600	Active TSS	Small Intestine	intestine
43	chr2:85804600-85805600	Bivalent/Poised TSS	HepG2	liver
44	chr2:85804600-85805800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
45	chr2:85804600-85805800	Active TSS	Breast Myoepithelial Primary Cells	Breast
46	chr2:85804600-85805800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr2:85804600-85805800	Enhancers	Psoas Muscle	Psoas
48	chr2:85804600-85805800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
49	chr2:85804600-85805800	Flanking Active TSS	HUVEC	blood vessel
50	chr2:85804600-85806000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links