Variant report

Variant	rs58725320
Chromosome Location	chr2:46686139-46686140
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:46673194..46677108-chr2:46685172..46689084,4	MCF-7	breast:
2	chr2:46524557..46526648-chr2:46685519..46687325,2	MCF-7	breast:
3	chr2:46654324..46657409-chr2:46685735..46688601,3	K562	blood:

Variant related genes	Relation type
ENSG00000116016	Chromatin interaction
ENSG00000241791	Chromatin interaction
ENSG00000187600	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs11125078	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12470939	0.94[EUR][1000 genomes]
rs12471274	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12473673	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12474961	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12474965	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12475015	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12612916	0.91[EUR][1000 genomes]
rs12613088	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12617193	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12619386	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12619696	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12619754	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12621486	0.86[EUR][1000 genomes]
rs12622818	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1530623	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1551123	0.89[EUR][1000 genomes]
rs1562454	0.89[EUR][1000 genomes]
rs17035200	0.86[EUR][1000 genomes]
rs1868095	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1868845	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2053766	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2121699	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2166746	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2276556	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2881326	0.91[EUR][1000 genomes]
rs34405528	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35589072	0.86[EUR][1000 genomes]
rs4145835	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4952825	0.88[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs4952826	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4952827	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4953364	0.91[EUR][1000 genomes]
rs4953370	0.94[EUR][1000 genomes]
rs4953376	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4953395	0.86[EUR][1000 genomes]
rs55871716	0.86[EUR][1000 genomes]
rs56894248	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57720200	0.90[ASN][1000 genomes]
rs57996107	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58402726	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59013670	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59761895	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59856996	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60685999	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61193538	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61560601	0.90[ASN][1000 genomes]
rs66533451	0.86[EUR][1000 genomes]
rs6714240	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6723195	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67739992	0.86[EUR][1000 genomes]
rs67960524	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs68030749	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72618620	0.91[EUR][1000 genomes]
rs72618621	0.91[EUR][1000 genomes]
rs72618622	0.94[EUR][1000 genomes]
rs72618623	0.94[EUR][1000 genomes]
rs72618624	0.94[EUR][1000 genomes]
rs72618625	0.94[EUR][1000 genomes]
rs72618626	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72618627	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72618628	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72618629	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72618631	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72618632	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72873772	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7573688	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7574467	0.94[EUR][1000 genomes]
rs7595513	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9710956	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012446	chr2:45921682-46737036	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	esv2757795	chr2:46532812-46874151	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv2759046	chr2:46532812-46874151	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	esv34650	chr2:46605659-46818992	Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	esv2756919	chr2:46614235-46756431	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
6	nsv437435	chr2:46636967-46763587	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	esv34937	chr2:46651624-46818586	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription 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	36 gene(s)	inside rSNPs	diseases
8	nsv581745	chr2:46660445-46693963	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
9	nsv9702	chr2:46668106-46745740	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
10	nsv817828	chr2:46670146-46739157	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
11	nsv1014425	chr2:46670179-47033417	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
12	nsv535678	chr2:46670179-47033417	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
13	nsv873996	chr2:46670941-47065227	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
14	nsv519216	chr2:46683683-46723219	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46667000-46688400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:46674600-46686600	Weak transcription	NHLF	lung
3	chr2:46679000-46687400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:46679600-46686400	Weak transcription	Right Atrium	heart
5	chr2:46680600-46687200	Weak transcription	Stomach Mucosa	stomach
6	chr2:46682800-46686400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr2:46684000-46688000	Weak transcription	K562	blood
8	chr2:46684200-46687000	Weak transcription	Pancreas	Pancrea
9	chr2:46684200-46687400	Weak transcription	Placenta	Placenta
10	chr2:46684800-46687600	Enhancers	HepG2	liver
11	chr2:46685400-46686400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr2:46685600-46686600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr2:46685800-46686800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr2:46685800-46688400	Enhancers	Stomach Smooth Muscle	stomach
15	chr2:46685800-46688600	Enhancers	Fetal Stomach	stomach
16	chr2:46686000-46686200	Weak transcription	Left Ventricle	heart
17	chr2:46686000-46686200	Weak transcription	Rectal Smooth Muscle	rectum
18	chr2:46686000-46687200	Enhancers	Brain Cingulate Gyrus	brain
19	chr2:46686000-46687200	Enhancers	Brain Substantia Nigra	brain
20	chr2:46686000-46687400	Enhancers	Brain Anterior Caudate	brain
21	chr2:46686000-46687400	Enhancers	Brain Hippocampus Middle	brain
22	chr2:46686000-46687800	Enhancers	Fetal Kidney	kidney
23	chr2:46686000-46688200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr2:46686000-46688600	Enhancers	Fetal Lung	lung
25	chr2:46686000-46689000	Enhancers	Adipose Nuclei	Adipose

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