Variant report

Variant	rs12636573
Chromosome Location	chr3:161006896-161006897
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:161000404..161005732-chr3:161006848..161011862,5	MCF-7	breast:
2	chr3:160818828..160822903-chr3:161006753..161012586,7	MCF-7	breast:
3	chr3:161006807..161008935-chr3:161043200..161045858,2	MCF-7	breast:
4	chr3:161006306..161018540-chr3:161080036..161092321,36	MCF-7	breast:
5	chr3:161006869..161011120-chr3:161039575..161043501,7	MCF-7	breast:
6	chr3:161006300..161011924-chr3:161012842..161019057,8	MCF-7	breast:
7	chr3:160990275..160995115-chr3:161003197..161013240,19	MCF-7	breast:
8	chr3:161003253..161016100-chr3:161121496..161137189,33	MCF-7	breast:
9	chr3:161006401..161012112-chr3:161031973..161037314,13	MCF-7	breast:
10	chr3:161004827..161016513-chr3:161081728..161095319,56	MCF-7	breast:
11	chr3:160992583..160995712-chr3:161006155..161008165,3	MCF-7	breast:
12	chr3:161006588..161008240-chr3:161008260..161009929,2	MCF-7	breast:
13	chr3:161001819..161012846-chr3:161052557..161065154,32	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NMD3-2	chr3:161006836-161007464	NONHSAT093012

No data

Variant related genes	Relation type
ENSG00000169251	Chromatin interaction
ENSG00000196542	Chromatin interaction
ENSG00000169255	Chromatin interaction
ENSG00000240138	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs11539155	0.95[EUR][1000 genomes]
rs12108169	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12374001	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12629152	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12629929	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12630038	0.95[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12631467	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12632346	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12633103	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12636434	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12636590	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1450530	0.85[EUR][1000 genomes]
rs16834031	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1904204	0.95[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs28384383	0.95[EUR][1000 genomes]
rs28853731	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4132373	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55949838	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56174161	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56741879	0.95[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs56890199	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs57441646	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs59827519	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60228180	0.95[AMR][1000 genomes]
rs60277631	0.94[AMR][1000 genomes]
rs60801542	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61193379	0.95[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs61388164	0.83[AMR][1000 genomes]
rs61578814	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61596736	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6800515	0.85[EUR][1000 genomes]
rs73875453	0.83[AMR][1000 genomes]
rs73875455	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73875456	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73875458	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs73875460	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73875464	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73875472	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73875473	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73875482	0.95[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs73875492	0.95[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs73875500	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73875502	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73878303	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73878304	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73878305	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7652447	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]

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	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv1015063	chr3:160918307-161024070	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv829770	chr3:160989573-161069223	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160994600-161016800	Weak transcription	Right Ventricle	heart
2	chr3:161003400-161008600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:161003400-161009200	Weak transcription	NHEK	skin
4	chr3:161003600-161008000	Weak transcription	Esophagus	oesophagus
5	chr3:161003600-161009000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr3:161003600-161009000	Weak transcription	HMEC	breast
7	chr3:161004000-161007200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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