Variant report

Variant	rs29538
Chromosome Location	chr7:41226502-41226503
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	chr7:41218957..41220551-chr7:41225375..41228012,2	MCF-7	breast:

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10233411	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10242681	0.89[CEU][hapmap]
rs10951647	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11768019	0.81[ASN][1000 genomes]
rs11975129	0.92[EUR][1000 genomes]
rs12670349	0.89[CEU][hapmap]
rs12701869	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12701875	0.86[CEU][hapmap]
rs13222193	0.89[CEU][hapmap]
rs13222281	0.92[CEU][hapmap]
rs13225532	0.89[ASN][1000 genomes]
rs13234888	0.89[CEU][hapmap]
rs13311231	0.81[ASN][1000 genomes]
rs255008	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs255009	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs255010	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs255012	0.89[ASN][1000 genomes]
rs255013	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs255014	0.89[ASN][1000 genomes]
rs255015	0.89[ASN][1000 genomes]
rs255016	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs255017	0.89[ASN][1000 genomes]
rs255018	0.93[EUR][1000 genomes]
rs28176	0.83[ASN][1000 genomes]
rs29519	0.83[ASN][1000 genomes]
rs29522	0.83[ASN][1000 genomes]
rs29523	0.81[ASN][1000 genomes]
rs29524	0.82[ASN][1000 genomes]
rs29530	0.89[ASN][1000 genomes]
rs29532	0.89[ASN][1000 genomes]
rs29533	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs29534	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs29535	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs29536	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs29537	0.91[ASN][1000 genomes]
rs29539	0.91[ASN][1000 genomes]
rs6951425	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs756439	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7796964	0.86[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv887989	chr7:41125447-41337044	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1028983	chr7:41165668-41635954	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv534465	chr7:41224437-41443498	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:41215200-41226600	Weak transcription	Aorta	Aorta
2	chr7:41215400-41230400	Weak transcription	Pancreas	Pancrea
3	chr7:41222600-41227600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr7:41225400-41231000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr7:41225600-41226800	Weak transcription	NHLF	lung
6	chr7:41225800-41226800	Weak transcription	NHDF-Ad	bronchial
7	chr7:41226000-41228000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr7:41226000-41231000	Enhancers	HUVEC	blood vessel
9	chr7:41226200-41227800	Enhancers	Hela-S3	cervix
10	chr7:41226400-41230400	Enhancers	Placenta	Placenta
11	chr7:41226400-41230600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr7:41226400-41230800	Enhancers	HMEC	breast
13	chr7:41226400-41231000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr7:41226400-41231000	Enhancers	NHEK	skin

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