Variant report

Variant	rs11899198
Chromosome Location	chr2:113840539-113840540
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFF	chr2:113840480-113840873	HepG2	liver:	n/a	chr2:113840774-113840792 chr2:113840780-113840794

No.	Distal block	Cell Line	Cell type
1	chr2:113838578..113840540-chr2:113849414..113851474,2	MCF-7	breast:
2	chr2:113840278..113841811-chr2:113847020..113849083,2	K562	blood:
3	chr2:113840365..113842107-chr2:113890479..113892989,2	MCF-7	breast:
4	chr2:113840473..113842575-chr2:113882514..113884830,2	MCF-7	breast:
5	chr2:113839317..113841682-chr2:113938699..113940328,2	K562	blood:
6	chr2:113741483..113743922-chr2:113839528..113841138,2	K562	blood:
7	chr2:113840523..113843293-chr2:113890844..113893174,3	MCF-7	breast:

Variant related genes	Relation type
RNU6-1180P	TF binding region

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10185781	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10207930	0.89[JPT][hapmap]
rs11123159	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11677407	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11681884	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11683132	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11684277	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11684289	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11684371	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11684719	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11686467	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11686511	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11687782	0.89[JPT][hapmap]
rs11688270	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11690459	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11883847	0.87[CEU][hapmap]
rs11886743	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11886754	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11887249	0.82[EUR][1000 genomes]
rs11891198	0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11893386	0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11897481	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11897709	0.82[EUR][1000 genomes]
rs11898158	0.85[EUR][1000 genomes]
rs13390577	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13406085	0.90[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13410552	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13432148	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1542176	0.82[CHD][hapmap];0.89[JPT][hapmap]
rs1623119	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17042721	0.87[CEU][hapmap]
rs17042750	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs17042810	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17042853	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17042888	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17042905	0.88[CEU][hapmap];0.89[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs17042917	0.88[CEU][hapmap];0.89[CHD][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs17486819	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs1992761	0.87[CEU][hapmap];0.80[EUR][1000 genomes]
rs1992762	0.82[EUR][1000 genomes]
rs1992763	0.80[EUR][1000 genomes]
rs2029582	0.80[CHD][hapmap];0.89[JPT][hapmap]
rs2121327	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2121329	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28928270	0.85[EUR][1000 genomes]
rs34466405	0.82[EUR][1000 genomes]
rs34517213	0.80[EUR][1000 genomes]
rs3811049	0.85[MEX][hapmap]
rs3811053	0.84[CHB][hapmap];0.86[CHD][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3811054	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4849152	0.86[CHD][hapmap]
rs55888413	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56060225	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56948778	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58036696	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58153729	0.87[ASN][1000 genomes]
rs58187820	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58922543	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59032902	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60341065	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60562399	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60924024	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60981695	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61366770	0.87[ASN][1000 genomes]
rs61546073	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6738377	0.89[JPT][hapmap]
rs72946783	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72946788	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72950839	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72950861	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72950867	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72950883	0.87[ASN][1000 genomes]
rs73955148	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73955151	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7561080	0.84[CHB][hapmap];0.88[JPT][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]

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	nsv532471	chr2:113682449-113862981	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv997348	chr2:113688093-113986508	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1007254	chr2:113726982-113887782	Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv535894	chr2:113726982-113887782	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv2881	chr2:113800805-113846597	Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113838200-113842200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:113838200-113842200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr2:113838200-113842200	Weak transcription	Stomach Mucosa	stomach
4	chr2:113838600-113842000	Weak transcription	NHEK	skin
5	chr2:113838800-113842000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr2:113839400-113843600	Weak transcription	Esophagus	oesophagus
7	chr2:113839600-113842200	Weak transcription	HMEC	breast
8	chr2:113840000-113842200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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