Variant report

Variant	rs4375086
Chromosome Location	chr9:21748332-21748333
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	chr9:21747038..21749658-chr9:21801876..21803848,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000099810	Chromatin interaction
ENSG00000264545	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10217131	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10217379	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.81[ASN][1000 genomes]
rs10429489	0.85[ASN][1000 genomes]
rs10511698	0.82[ASN][1000 genomes]
rs10511699	0.82[ASN][1000 genomes]
rs10511700	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10757256	0.87[ASN][1000 genomes]
rs10811593	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10811594	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10811606	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10811607	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10811609	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10811616	0.84[ASN][1000 genomes]
rs10811619	0.82[ASN][1000 genomes]
rs10811624	0.90[CEU][hapmap]
rs10811631	0.85[JPT][hapmap]
rs10965118	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10965124	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10965131	0.86[ASN][1000 genomes]
rs10965150	0.90[CEU][hapmap]
rs11496368	0.84[EUR][1000 genomes]
rs12004745	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs12336678	0.86[ASN][1000 genomes]
rs12336734	0.86[ASN][1000 genomes]
rs12337510	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap]
rs12340988	0.82[ASN][1000 genomes]
rs12348845	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12378675	0.89[CEU][hapmap]
rs12379110	0.83[ASN][1000 genomes]
rs12380373	0.83[ASN][1000 genomes]
rs13286524	0.82[ASN][1000 genomes]
rs13302653	0.83[CEU][hapmap];0.92[JPT][hapmap]
rs1414258	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1414259	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1440992	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1544195	0.90[CEU][hapmap]
rs2039971	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs2282245	0.83[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap]
rs2383184	0.83[ASN][1000 genomes]
rs35235093	0.84[ASN][1000 genomes]
rs35526535	0.82[ASN][1000 genomes]
rs3931609	0.83[CEU][hapmap];0.92[JPT][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap]
rs4326466	0.87[ASN][1000 genomes]
rs4543632	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55656405	0.85[ASN][1000 genomes]
rs6475567	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6475575	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6475580	0.87[ASN][1000 genomes]
rs6475581	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.82[TSI][hapmap];0.82[ASN][1000 genomes]
rs6475582	0.82[ASN][1000 genomes]
rs6475583	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6475584	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs66846966	0.87[ASN][1000 genomes]
rs7029287	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7033148	0.81[ASN][1000 genomes]
rs7037277	0.81[ASN][1000 genomes]
rs7040432	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7040895	0.85[ASN][1000 genomes]
rs7042728	0.83[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap]
rs7042884	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7045771	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7048433	0.83[ASN][1000 genomes]
rs7846904	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7850447	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7851125	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap]
rs7860126	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap]
rs7866362	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7866533	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7866860	0.82[ASN][1000 genomes]
rs7867176	0.91[CEU][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap]
rs7868253	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7871477	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs7871631	0.85[ASN][1000 genomes]
rs7874112	0.83[CEU][hapmap];0.92[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs885518	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap]
rs9298826	0.82[ASN][1000 genomes]
rs945263	0.82[AMR][1000 genomes];0.87[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	nsv1029634	chr9:21542970-21765286	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv892743	chr9:21675545-21772064	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv529609	chr9:21708371-22537069	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv1026981	chr9:21748202-21811697	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21743200-21750000	Weak transcription	NH-A	brain
2	chr9:21743400-21750000	Weak transcription	Osteobl	bone
3	chr9:21744200-21752200	Enhancers	HMEC	breast
4	chr9:21745000-21748800	Enhancers	NHEK	skin
5	chr9:21746600-21748600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr9:21746600-21748800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr9:21746600-21751200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr9:21746800-21748400	Enhancers	Hela-S3	cervix
9	chr9:21747000-21750000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr9:21747200-21752000	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr9:21747600-21750000	Weak transcription	NHDF-Ad	bronchial
12	chr9:21747800-21749800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr9:21747800-21751800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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