Variant report

Variant	rs12996636
Chromosome Location	chr2:56461523-56461524
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1001471	1.00[ASW][hapmap];0.87[GIH][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10188465	0.90[CHB][hapmap]
rs10490397	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10490401	0.81[EUR][1000 genomes]
rs11125618	0.90[CHB][hapmap];0.83[CHD][hapmap]
rs12613716	0.95[CHB][hapmap];0.89[CHD][hapmap];0.94[MEX][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12613794	0.80[CHB][hapmap]
rs12623053	0.90[CHB][hapmap]
rs12623278	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.93[MEX][hapmap];0.96[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12713316	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12993884	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12994087	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13003301	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13012528	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.93[MEX][hapmap];0.96[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13403828	0.95[CHB][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13429808	0.95[CHB][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1468914	0.90[CHB][hapmap];0.83[CHD][hapmap]
rs17047656	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17047684	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17047705	0.90[CHB][hapmap]
rs2111476	0.85[CHB][hapmap];0.90[GIH][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2216325	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs35637593	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57041406	0.81[EUR][1000 genomes]
rs6710311	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6730327	0.89[CHB][hapmap]
rs7563888	0.95[CHB][hapmap]
rs7576428	0.90[CHB][hapmap]
rs7590310	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7591193	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7591392	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs759615	0.85[CHB][hapmap]
rs7602551	0.85[CHB][hapmap]
rs9653542	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs969301	1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs969302	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs969303	0.90[CHB][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	esv2757799	chr2:56178439-56472394	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
2	esv2759051	chr2:56178439-56472394	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
3	nsv874162	chr2:56255832-56480571	Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv874169	chr2:56383762-56473480	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv530516	chr2:56447922-56633505	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	2 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	chr2:56458200-56466000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr2:56459800-56462200	Enhancers	HUES6 Cell Line	embryonic stem cell
3	chr2:56460200-56462600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr2:56460600-56461800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr2:56460800-56461600	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr2:56461200-56461600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
7	chr2:56461200-56461600	Active TSS	HSMMtube	muscle
8	chr2:56461400-56461600	Active TSS	HSMM	muscle

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