Variant report

Variant	rs3811608
Chromosome Location	chr2:191335057-191335058
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:191318515..191323057-chr2:191332501..191335066,4	MCF-7	breast:
2	chr2:191272262..191274939-chr2:191333629..191335814,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151690	Chromatin interaction
ENSG00000272979	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10169169	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10171376	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10173975	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10179262	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10185147	0.94[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10189140	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10202274	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10204342	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10208737	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10209340	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs10211375	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10737936	0.83[CEU][hapmap];0.82[CHB][hapmap]
rs11553601	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11695439	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs13031452	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13384743	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13386210	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13388162	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13395233	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13398741	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13405215	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13410179	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13412663	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13412823	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13412835	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13412879	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13417310	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13418943	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13421959	1.00[YRI][hapmap]
rs13429315	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1837686	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4283453	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4853712	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs56715527	0.86[ASN][1000 genomes]
rs58210597	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58253207	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58433478	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58708643	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6434401	0.83[CEU][hapmap];0.82[CHB][hapmap]
rs6717050	0.95[ASN][1000 genomes]
rs72903349	0.85[ASN][1000 genomes]
rs72903383	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72905242	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73054092	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7556716	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7560045	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7562013	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7564107	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7574844	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7584379	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7594994	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7609330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs894072	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs8962	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9288174	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9967829	0.83[CEU][hapmap];0.82[CHB][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33134	chr2:191318791-191365710	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3811608	FLJ20160	cis	multi-tissue	Pritchard
rs3811608	FLJ20160	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:191306600-191351000	Weak transcription	Pancreas	Pancrea
2	chr2:191322000-191335800	Weak transcription	Esophagus	oesophagus
3	chr2:191322600-191335600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr2:191323200-191335800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr2:191325600-191335800	Weak transcription	Lung	lung
6	chr2:191325600-191346200	Weak transcription	Right Ventricle	heart
7	chr2:191327600-191353000	Weak transcription	Primary B cells from cord blood	blood
8	chr2:191330600-191335200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr2:191330800-191335400	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr2:191330800-191335400	Enhancers	Rectal Mucosa Donor 31	rectum
11	chr2:191331000-191335200	Enhancers	Brain Cingulate Gyrus	brain
12	chr2:191331000-191335400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr2:191331000-191335400	Enhancers	Hela-S3	cervix
14	chr2:191331000-191335400	Enhancers	Osteobl	bone
15	chr2:191331200-191335400	Enhancers	NHLF	lung
16	chr2:191331200-191335600	Enhancers	Fetal Lung	lung
17	chr2:191331400-191335200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr2:191331400-191335200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr2:191331400-191335400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr2:191331400-191335400	Enhancers	Brain Angular Gyrus	brain
21	chr2:191331400-191335400	Enhancers	Fetal Heart	heart
22	chr2:191331400-191335400	Enhancers	Fetal Muscle Leg	muscle
23	chr2:191331400-191335400	Enhancers	Fetal Stomach	stomach
24	chr2:191331400-191335600	Enhancers	Colon Smooth Muscle	Colon
25	chr2:191331600-191335400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr2:191331600-191335400	Enhancers	Stomach Mucosa	stomach
27	chr2:191331600-191335600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr2:191331800-191335400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr2:191332400-191335400	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr2:191332400-191335400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr2:191332400-191335400	Enhancers	Fetal Intestine Small	intestine
32	chr2:191332400-191335400	Enhancers	HMEC	breast
33	chr2:191332400-191335400	Enhancers	NHEK	skin
34	chr2:191332600-191335400	Enhancers	Primary hematopoietic stem cells	blood
35	chr2:191332600-191336000	Enhancers	Fetal Intestine Large	intestine
36	chr2:191332800-191336000	Enhancers	Brain Anterior Caudate	brain
37	chr2:191332800-191356200	Weak transcription	Aorta	Aorta
38	chr2:191332800-191364200	Weak transcription	Spleen	Spleen
39	chr2:191333000-191336000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr2:191333400-191335400	Enhancers	HUVEC	blood vessel
41	chr2:191333400-191342600	Weak transcription	Gastric	stomach
42	chr2:191333400-191355400	Weak transcription	Fetal Muscle Trunk	muscle
43	chr2:191333600-191335200	Enhancers	Primary monocytes fromperipheralblood	blood
44	chr2:191333600-191342600	Weak transcription	Colonic Mucosa	Colon
45	chr2:191333800-191335200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
46	chr2:191333800-191335800	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr2:191333800-191342600	Weak transcription	Left Ventricle	heart
48	chr2:191334200-191335400	Enhancers	Brain Hippocampus Middle	brain
49	chr2:191334200-191335400	Enhancers	A549	lung
50	chr2:191334200-191342600	Weak transcription	Fetal Brain Female	brain

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