Variant report

Variant	rs2087849
Chromosome Location	chr4:142638211-142638212
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:142295670..142297489-chr4:142636919..142639486,2	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10010469	1.00[ASN][1000 genomes]
rs10028670	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1040257	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11100724	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12508955	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13111860	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1493024	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1500835	1.00[ASN][1000 genomes]
rs1519552	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs1519553	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1589241	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs1607592	0.87[EUR][1000 genomes]
rs1607593	0.88[EUR][1000 genomes]
rs1850853	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2254514	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2322262	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs4055041	1.00[ASN][1000 genomes]
rs4956305	1.00[ASN][1000 genomes]
rs4956404	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4956407	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6537058	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs6816210	0.91[CEU][hapmap]
rs6837991	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs6841454	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7661408	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7688250	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7698675	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs937177	1.00[ASN][1000 genomes]
rs990851	0.95[CEU][hapmap];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv880173	chr4:142355535-142666106	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	esv3401979	chr4:142434442-142803321	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1018949	chr4:142451823-142732365	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1030822	chr4:142487721-142706053	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1027004	chr4:142487721-143007320	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv498005	chr4:142515689-143502988	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	esv3448093	chr4:142612197-142704695	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:142608800-142655000	Weak transcription	Gastric	stomach
2	chr4:142624000-142652000	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr4:142624200-142651000	Weak transcription	Stomach Smooth Muscle	stomach
4	chr4:142629400-142651000	Weak transcription	Left Ventricle	heart
5	chr4:142629400-142654600	Weak transcription	Esophagus	oesophagus
6	chr4:142629400-142655000	Weak transcription	Spleen	Spleen
7	chr4:142629600-142657600	Weak transcription	Right Ventricle	heart
8	chr4:142630000-142638600	Weak transcription	Aorta	Aorta
9	chr4:142630000-142650400	Weak transcription	Primary B cells from peripheral blood	blood
10	chr4:142634600-142653600	Weak transcription	Colon Smooth Muscle	Colon
11	chr4:142634800-142641600	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr4:142634800-142656200	Weak transcription	Pancreas	Pancrea
13	chr4:142635800-142651600	Weak transcription	NHDF-Ad	bronchial
14	chr4:142635800-142651800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr4:142635800-142651800	Weak transcription	HSMM	muscle
16	chr4:142635800-142651800	Weak transcription	NHLF	lung
17	chr4:142635800-142651800	Weak transcription	Osteobl	bone
18	chr4:142635800-142653600	Weak transcription	HSMMtube	muscle
19	chr4:142636000-142642200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr4:142636200-142642200	Weak transcription	A549	lung
21	chr4:142636200-142642800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr4:142636200-142647200	Weak transcription	Hela-S3	cervix
23	chr4:142637400-142638600	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr4:142637400-142651000	Weak transcription	Rectal Smooth Muscle	rectum
25	chr4:142637800-142639400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr4:142638000-142638600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links