Variant report

Variant	rs11125515
Chromosome Location	chr2:53886799-53886800
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:53883186..53885519-chr2:53886263..53888852,2	K562	blood:
2	chr2:53883597..53885623-chr2:53885808..53888099,2	MCF-7	breast:
3	chr2:53882348..53885519-chr2:53886263..53888852,3	K562	blood:

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10188142	0.82[GIH][hapmap]
rs10865275	0.83[AFR][1000 genomes]
rs11682721	0.82[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs11684084	0.85[CHB][hapmap];0.86[ASN][1000 genomes]
rs11889094	0.96[ASN][1000 genomes]
rs11896043	0.81[AFR][1000 genomes]
rs11902691	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12611475	0.93[ASN][1000 genomes]
rs12620583	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12621225	0.81[JPT][hapmap]
rs13414216	0.81[JPT][hapmap]
rs2080715	0.83[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2111623	0.81[JPT][hapmap]
rs2111852	0.82[AMR][1000 genomes]
rs2160929	0.91[CHB][hapmap];0.86[JPT][hapmap];0.96[ASN][1000 genomes]
rs2160930	0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs2193682	0.86[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs2193683	0.86[ASN][1000 genomes]
rs2357693	0.81[CHD][hapmap]
rs2542584	0.81[JPT][hapmap]
rs2542585	0.81[JPT][hapmap]
rs2542588	0.81[JPT][hapmap]
rs2692532	0.80[JPT][hapmap]
rs2692536	0.81[JPT][hapmap]
rs2949812	0.81[JPT][hapmap]
rs3770403	0.83[ASN][1000 genomes]
rs3770405	0.82[ASN][1000 genomes]
rs3821081	0.81[CHD][hapmap]
rs56081372	0.90[ASN][1000 genomes]
rs56291505	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62139772	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62139780	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62139783	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs62139835	0.80[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6705712	0.82[CEU][hapmap];0.84[CHD][hapmap];0.82[GIH][hapmap];0.84[TSI][hapmap]
rs6713107	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6714891	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6727876	0.84[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs6728355	0.80[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6741239	0.95[ASN][1000 genomes]
rs6743627	0.91[CHB][hapmap];0.94[CHD][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs6757393	0.93[ASN][1000 genomes]
rs7556791	0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7557799	0.91[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs7557898	0.85[CHB][hapmap];0.94[CHD][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs7563054	0.81[ASW][hapmap];0.95[CEU][hapmap];0.85[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.95[MKK][hapmap];0.94[TSI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7584474	0.92[ASN][1000 genomes]
rs7587217	0.92[ASN][1000 genomes]
rs7601692	0.81[JPT][hapmap]
rs805438	0.81[JPT][hapmap]
rs918207	0.81[CHD][hapmap];0.80[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916267	chr2:53747525-53955999	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv874147	chr2:53772561-53886799	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv984439	chr2:53861720-53955437	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1003263	chr2:53863287-54055359	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv535720	chr2:53863287-54055359	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:53874200-53935000	Weak transcription	Pancreas	Pancrea
2	chr2:53879400-53895600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr2:53881200-53895800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr2:53881400-53934400	Weak transcription	Stomach Smooth Muscle	stomach
5	chr2:53881800-53896400	Weak transcription	Aorta	Aorta
6	chr2:53882600-53888200	Weak transcription	Colon Smooth Muscle	Colon
7	chr2:53882600-53894000	Weak transcription	Fetal Stomach	stomach
8	chr2:53882800-53895600	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr2:53883200-53897800	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr2:53883600-53896600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr2:53885000-53895800	Weak transcription	Dnd41	blood
12	chr2:53885600-53925000	Weak transcription	Fetal Intestine Small	intestine
13	chr2:53885800-53911800	Weak transcription	Adipose Nuclei	Adipose
14	chr2:53886000-53888000	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr2:53886400-53886800	Bivalent Enhancer	Psoas Muscle	Psoas
16	chr2:53886400-53887000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr2:53886600-53896400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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