Variant report

Variant	rs2005548
Chromosome Location	chr7:99346373-99346374
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	chr7:99341182..99342708-chr7:99343739..99346587,2	MCF-7	breast:

Extended variants
information (count: 90 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10211	0.90[CHB][hapmap]
rs10242455	0.85[CHB][hapmap]
rs10282706	0.80[CHB][hapmap]
rs12360	0.90[CHB][hapmap]
rs1357319	0.90[CHB][hapmap];0.80[ASN][1000 genomes]
rs1419745	0.95[CHB][hapmap];0.83[CHD][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs15524	0.85[CHB][hapmap]
rs17161774	0.95[CHB][hapmap];0.87[JPT][hapmap]
rs17161780	0.90[CHB][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap]
rs17161783	0.95[CHB][hapmap];0.89[GIH][hapmap];0.85[MEX][hapmap]
rs17161880	1.00[EUR][1000 genomes]
rs1851427	0.90[ASN][1000 genomes]
rs1859690	0.85[CHB][hapmap]
rs1879859	0.90[CHB][hapmap]
rs2037497	0.80[ASN][1000 genomes]
rs2037498	0.90[CHB][hapmap];0.80[ASN][1000 genomes]
rs2037499	0.90[CHB][hapmap];0.80[ASN][1000 genomes]
rs2090949	0.80[ASN][1000 genomes]
rs2140128	0.80[ASN][1000 genomes]
rs2222411	0.90[CHB][hapmap];0.80[ASN][1000 genomes]
rs2257401	0.90[CHB][hapmap]
rs2404769	0.80[ASN][1000 genomes]
rs2404770	0.90[CHB][hapmap];0.80[ASN][1000 genomes]
rs2687072	0.80[ASN][1000 genomes]
rs2687075	0.90[CHB][hapmap]
rs2687076	0.90[CHB][hapmap]
rs2687079	0.90[CHB][hapmap]
rs2687081	0.83[CHB][hapmap]
rs2687086	0.90[CHB][hapmap]
rs2687087	0.90[CHB][hapmap]
rs2687133	0.90[CHB][hapmap];0.82[ASN][1000 genomes]
rs2687134	0.90[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs2687135	0.80[ASN][1000 genomes]
rs2687136	0.90[CHB][hapmap];0.80[ASN][1000 genomes]
rs2687137	0.80[ASN][1000 genomes]
rs2687139	0.90[CHB][hapmap];0.80[ASN][1000 genomes]
rs2687140	0.87[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs2687141	0.80[ASN][1000 genomes]
rs2687142	0.90[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs2687143	0.80[ASN][1000 genomes]
rs2687144	0.90[CHB][hapmap];0.80[ASN][1000 genomes]
rs2687145	0.90[CHB][hapmap];0.80[ASN][1000 genomes]
rs2740558	0.80[ASN][1000 genomes]
rs2740559	0.80[ASN][1000 genomes]
rs2740560	0.80[ASN][1000 genomes]
rs2740561	0.89[CHB][hapmap];0.80[ASN][1000 genomes]
rs2740565	0.90[CHB][hapmap]
rs2741872	0.82[ASN][1000 genomes]
rs34880695	1.00[EUR][1000 genomes]
rs35909867	1.00[EUR][1000 genomes]
rs35974388	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35984428	1.00[EUR][1000 genomes]
rs3735453	0.85[CHB][hapmap]
rs3800960	0.85[GIH][hapmap];0.85[MEX][hapmap]
rs3823812	0.83[ASN][1000 genomes]
rs45442295	0.92[ASN][1000 genomes]
rs45600842	0.92[ASN][1000 genomes]
rs45624139	0.80[ASN][1000 genomes]
rs4646446	1.00[CHB][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];0.87[JPT][hapmap];0.85[MEX][hapmap];0.83[ASN][1000 genomes]
rs4646447	0.95[CHB][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];0.87[JPT][hapmap];0.85[MEX][hapmap];0.82[ASN][1000 genomes]
rs4646449	0.95[CHB][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];0.87[JPT][hapmap];0.85[MEX][hapmap];0.82[ASN][1000 genomes]
rs4646450	0.80[CHB][hapmap]
rs4646453	0.95[CHB][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];0.87[JPT][hapmap];0.85[MEX][hapmap];0.82[ASN][1000 genomes]
rs4646456	0.95[CHB][hapmap];0.89[GIH][hapmap];0.85[MEX][hapmap]
rs4646457	0.85[CHB][hapmap]
rs4646458	0.95[CHB][hapmap]
rs4646461	0.82[ASN][1000 genomes]
rs4646462	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55852703	0.80[ASN][1000 genomes]
rs58024720	0.82[ASN][1000 genomes]
rs58649180	0.82[ASN][1000 genomes]
rs59172435	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60298785	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61593387	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6465750	0.85[CHB][hapmap]
rs72494453	0.88[ASN][1000 genomes]
rs72494454	0.90[ASN][1000 genomes]
rs72494455	0.82[ASN][1000 genomes]
rs72494456	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72494458	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73410654	0.80[ASN][1000 genomes]
rs776741	1.00[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs776746	0.85[CHB][hapmap]
rs7798931	0.81[ASN][1000 genomes]
rs7808022	0.85[CHB][hapmap]
rs939955	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[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	nsv482532	chr7:99205906-99363886	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv888771	chr7:99294762-99355278	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	esv3331003	chr7:99337054-99386069	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	esv3450108	chr7:99339737-99383419	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 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	chr7:99311800-99349000	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr7:99339200-99346400	Weak transcription	Aorta	Aorta
3	chr7:99339200-99352200	Weak transcription	Left Ventricle	heart
4	chr7:99340000-99346600	Weak transcription	Hela-S3	cervix
5	chr7:99341000-99348000	Weak transcription	Pancreas	Pancrea
6	chr7:99345800-99348200	Weak transcription	HepG2	liver
7	chr7:99346000-99346800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr7:99346000-99347400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr7:99346200-99350200	Enhancers	Placenta Amnion	Placenta Amnion

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