Variant report

Variant	rs953641
Chromosome Location	chr3:142427736-142427737
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	chr3:142296287..142298547-chr3:142424525..142428027,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000175054	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11715459	0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1382688	1.00[CEU][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes]
rs2033912	1.00[CEU][hapmap];0.97[TSI][hapmap]
rs2049328	1.00[CEU][hapmap];0.89[CHB][hapmap];0.91[EUR][1000 genomes]
rs2177398	1.00[CEU][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes]
rs2354856	1.00[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];0.82[AMR][1000 genomes]
rs28571594	0.97[ASN][1000 genomes]
rs28658009	0.82[AMR][1000 genomes]
rs28689551	0.82[AMR][1000 genomes]
rs3821647	0.87[CEU][hapmap];0.83[CHB][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap]
rs3844273	0.84[TSI][hapmap]
rs4259003	0.87[CEU][hapmap];0.88[CHB][hapmap];0.91[TSI][hapmap]
rs4530572	0.86[EUR][1000 genomes]
rs4643748	1.00[CEU][hapmap];0.82[AMR][1000 genomes]
rs6440104	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6440105	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6440108	1.00[CEU][hapmap]
rs66813358	0.81[AMR][1000 genomes]
rs66897945	0.90[AMR][1000 genomes]
rs67100994	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67495151	0.81[AMR][1000 genomes]
rs6772222	0.82[AMR][1000 genomes]
rs6798849	0.82[AMR][1000 genomes]
rs6803681	1.00[CEU][hapmap];0.82[AMR][1000 genomes]
rs7621642	1.00[CEU][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes]
rs7623762	0.94[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs7623977	0.80[AMR][1000 genomes]
rs7629129	0.92[ASN][1000 genomes]
rs7631245	0.83[CHB][hapmap]
rs7635768	0.82[EUR][1000 genomes]
rs7637826	0.82[EUR][1000 genomes]
rs7637846	1.00[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap]
rs7638459	1.00[CEU][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes]
rs7639403	1.00[CEU][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes]
rs7641514	1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.97[TSI][hapmap]
rs7653309	0.82[AMR][1000 genomes]
rs7772	0.86[TSI][hapmap]
rs953239	0.94[CHB][hapmap];1.00[CHD][hapmap];0.87[JPT][hapmap]
rs9815607	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes]
rs9824476	0.82[AMR][1000 genomes]
rs9835135	0.82[AMR][1000 genomes]
rs9836269	1.00[CEU][hapmap]
rs9849461	1.00[CEU][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes]
rs9851381	0.86[CEU][hapmap]
rs9864230	1.00[CEU][hapmap];0.82[AMR][1000 genomes]
rs9868886	1.00[CEU][hapmap];0.83[CHB][hapmap]

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	nsv591920	chr3:142411200-142496951	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv521098	chr3:142411200-142503605	Weak transcription Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv520533	chr3:142417070-142440299	Weak transcription Strong transcription Enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv518623	chr3:142417070-142503605	Weak transcription Active TSS Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142366000-142435400	Weak transcription	Colonic Mucosa	Colon
2	chr3:142389800-142442400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr3:142392800-142433000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr3:142408800-142430400	Weak transcription	Liver	Liver
5	chr3:142424600-142430200	Weak transcription	Duodenum Mucosa	Duodenum
6	chr3:142425800-142431000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr3:142426200-142435000	Weak transcription	Fetal Intestine Large	intestine
8	chr3:142427000-142430600	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr3:142427000-142430600	Weak transcription	Rectal Mucosa Donor 31	rectum

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