Variant report

Variant	rs12041985
Chromosome Location	chr1:56081956-56081957
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:56080025..56082249-chr1:56093163..56095810,2	K562	blood:

Extended variants
information (count: 43 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10493196	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs10749702	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11206625	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11206629	1.00[CEU][hapmap];0.81[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11206636	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11206637	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11206638	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11206639	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11807964	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12026971	0.96[CEU][hapmap];0.80[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12040862	1.00[CEU][hapmap];0.85[JPT][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12086546	0.82[EUR][1000 genomes]
rs12132336	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12139752	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12142554	0.85[EUR][1000 genomes]
rs12401977	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs1392128	1.00[CEU][hapmap];0.80[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1392129	1.00[CEU][hapmap];0.81[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1392130	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1392131	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1392132	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1587432	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1604016	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17112402	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs17417716	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56169646	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61776360	0.85[EUR][1000 genomes]
rs61776375	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61776377	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6669248	0.85[EUR][1000 genomes]
rs709397	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7513395	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7525515	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7544458	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7546899	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7555929	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7556008	0.86[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs769971	0.99[ASN][1000 genomes]
rs769984	0.99[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	nsv10184	chr1:55728755-56084833	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv461617	chr1:56055190-56123510	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	nsv546303	chr1:56055190-56123510	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv1014866	chr1:56059054-56129092	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:56063200-56089000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:56077200-56086000	Weak transcription	Aorta	Aorta
3	chr1:56079200-56083800	Weak transcription	HSMM	muscle
4	chr1:56079400-56082400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:56080800-56082800	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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