Variant report

Variant	rs3770090
Chromosome Location	chr2:86263288-86263289
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:86054291..86055159-chr2:86262823..86263723,2	MCF-7	breast:
2	chr2:86263075..86266284-chr2:86266783..86270779,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000068654	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10165327	0.86[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs10168635	0.82[ASN][1000 genomes]
rs10174095	1.00[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.87[ASN][1000 genomes]
rs10179090	0.82[ASN][1000 genomes]
rs1019591	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1036554	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10427394	0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs11884765	0.92[GIH][hapmap]
rs11899576	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12612513	0.94[ASN][1000 genomes]
rs12614260	0.94[ASN][1000 genomes]
rs12620810	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs12621992	1.00[CEU][hapmap]
rs12622009	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12622715	1.00[CEU][hapmap];0.84[CHB][hapmap]
rs12624126	1.00[CEU][hapmap]
rs13384563	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13390702	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1559516	0.86[CHB][hapmap];0.93[JPT][hapmap]
rs1561328	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];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17026701	1.00[CEU][hapmap]
rs17026729	1.00[CEU][hapmap]
rs17026854	0.96[ASN][1000 genomes]
rs17026940	0.92[GIH][hapmap]
rs17027011	0.82[ASN][1000 genomes]
rs17584578	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.94[ASN][1000 genomes]
rs17618001	1.00[CEU][hapmap];0.94[ASN][1000 genomes]
rs2012798	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2118521	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2164879	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2228352	0.92[GIH][hapmap]
rs2241435	1.00[CEU][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs2241437	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.89[ASN][1000 genomes]
rs2278085	0.96[ASN][1000 genomes]
rs2278087	0.94[ASN][1000 genomes]
rs2278088	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.94[ASN][1000 genomes]
rs2288121	0.85[CHB][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs2289237	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2303339	1.00[CEU][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs2303340	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.92[ASN][1000 genomes]
rs311562	0.84[ASN][1000 genomes]
rs311566	0.84[ASN][1000 genomes]
rs311567	0.86[CHB][hapmap];0.83[CHD][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs34522092	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3731819	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.90[ASN][1000 genomes]
rs3770066	0.82[ASN][1000 genomes]
rs3770081	0.90[ASN][1000 genomes]
rs3770087	1.00[CEU][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]
rs3770089	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3810827	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3815840	0.84[ASN][1000 genomes]
rs4832242	0.86[CHB][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs4832250	0.86[CHB][hapmap];0.83[CHD][hapmap];0.93[JPT][hapmap]
rs56104203	0.92[ASN][1000 genomes]
rs56326127	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56977454	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57083584	0.94[ASN][1000 genomes]
rs57398459	0.94[ASN][1000 genomes]
rs58186343	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58365138	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58898686	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59835600	0.92[ASN][1000 genomes]
rs59891296	0.99[AFR][1000 genomes]
rs60649958	0.94[ASN][1000 genomes]
rs6750765	0.91[ASN][1000 genomes]
rs73943946	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73947314	0.96[ASN][1000 genomes]
rs7562837	0.81[AMR][1000 genomes]
rs7608262	0.98[ASN][1000 genomes]
rs918857	0.94[AFR][1000 genomes]
rs918858	0.92[AFR][1000 genomes]
rs9789563	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9973880	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001104	chr2:86182021-86271923	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv535807	chr2:86182021-86271923	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv2751903	chr2:86253542-86505453	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv531380	chr2:86253552-86469217	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3770090	LOC90784	cis	lymphoblastoid	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86245400-86263400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:86251200-86273200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
3	chr2:86251200-86281400	Strong transcription	H9 Cell Line	embryonic stem cell
4	chr2:86251200-86283000	Strong transcription	HepG2	liver
5	chr2:86251200-86283200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr2:86251200-86285000	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr2:86251200-86285200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr2:86251400-86263400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr2:86252000-86331200	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr2:86252200-86282600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
11	chr2:86252200-86285200	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr2:86252400-86283200	Strong transcription	H1 Cell Line	embryonic stem cell
13	chr2:86252600-86267800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
14	chr2:86252600-86276800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr2:86254400-86263600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr2:86257200-86264400	Strong transcription	K562	blood
17	chr2:86258200-86265400	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr2:86260000-86263400	Genic enhancers	Fetal Muscle Leg	muscle
19	chr2:86260200-86266200	Genic enhancers	Fetal Stomach	stomach
20	chr2:86260600-86265000	Enhancers	Fetal Heart	heart
21	chr2:86260600-86268800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr2:86260600-86269000	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr2:86260800-86264200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr2:86260800-86268800	Weak transcription	Ovary	ovary
25	chr2:86261200-86263400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
26	chr2:86261200-86272000	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr2:86261400-86263400	Enhancers	Primary B cells from peripheral blood	blood
28	chr2:86261400-86265600	Enhancers	Left Ventricle	heart
29	chr2:86261400-86266200	Enhancers	Psoas Muscle	Psoas
30	chr2:86261600-86265600	Enhancers	Right Ventricle	heart
31	chr2:86261800-86266400	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr2:86262000-86265800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr2:86262200-86264400	Enhancers	Liver	Liver
34	chr2:86262400-86263400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr2:86262400-86263400	Genic enhancers	Adipose Nuclei	Adipose
36	chr2:86262400-86263400	Genic enhancers	Brain Cingulate Gyrus	brain
37	chr2:86262400-86263400	Enhancers	HUVEC	blood vessel
38	chr2:86262400-86264000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr2:86262400-86264200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
40	chr2:86262400-86264200	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr2:86262400-86264400	Enhancers	Brain Anterior Caudate	brain
42	chr2:86262400-86265200	Enhancers	Spleen	Spleen
43	chr2:86262400-86265200	Genic enhancers	NHEK	skin
44	chr2:86262400-86266000	Genic enhancers	Brain Angular Gyrus	brain
45	chr2:86262400-86266000	Genic enhancers	Fetal Intestine Small	intestine
46	chr2:86262400-86266000	Enhancers	Right Atrium	heart
47	chr2:86262400-86266200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr2:86262400-86266200	Enhancers	Lung	lung
49	chr2:86262400-86266800	Genic enhancers	Placenta	Placenta
50	chr2:86262400-86268400	Flanking Active TSS	Thymus	Thymus

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