Variant report

Variant	rs58402726
Chromosome Location	chr2:46705064-46705065
allele	C/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	SETDB1	chr2:46704865-46705248	U2OS	brain:	n/a	n/a
2	FOXA2	chr2:46704618-46705122	A549	lung:	n/a	n/a
3	KAP1	chr2:46704853-46705281	HEK293	kidney:	n/a	n/a
4	STAT3	chr2:46704975-46705107	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:46656214..46657827-chr2:46704173..46707018,3	K562	blood:
2	chr2:46703332..46705552-chr2:46707048..46709063,2	K562	blood:
3	chr2:46704470..46707025-chr2:46769256..46770963,2	MCF-7	breast:

Variant related genes	Relation type
TMEM247	TF binding region
ENSG00000187600	Chromatin interaction
ENSG00000119729	Chromatin interaction
ENSG00000250565	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs11125078	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12470939	0.88[EUR][1000 genomes]
rs12471274	0.86[EUR][1000 genomes]
rs12473673	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12474961	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12474965	0.83[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs12475015	0.86[AMR][1000 genomes]
rs12612916	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12613088	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12617193	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12619386	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12619696	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12619754	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12621486	0.86[EUR][1000 genomes]
rs12622818	0.91[EUR][1000 genomes]
rs1530623	0.88[EUR][1000 genomes]
rs1551123	0.89[EUR][1000 genomes]
rs1562454	0.89[EUR][1000 genomes]
rs17035200	0.91[EUR][1000 genomes]
rs1868095	0.83[EUR][1000 genomes]
rs1868845	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2053766	0.88[EUR][1000 genomes]
rs2121699	0.83[EUR][1000 genomes]
rs2166746	0.88[EUR][1000 genomes]
rs2276556	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2881326	0.85[EUR][1000 genomes]
rs34405528	0.80[EUR][1000 genomes]
rs35589072	0.86[EUR][1000 genomes]
rs4145835	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4952825	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4952826	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4952827	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4953364	0.86[EUR][1000 genomes]
rs4953370	0.88[EUR][1000 genomes]
rs4953376	0.88[EUR][1000 genomes]
rs4953395	0.91[EUR][1000 genomes]
rs55871716	0.91[EUR][1000 genomes]
rs56894248	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57996107	0.86[EUR][1000 genomes]
rs58725320	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59013670	0.91[EUR][1000 genomes]
rs59761895	0.85[AFR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59856996	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60685999	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61193538	0.86[EUR][1000 genomes]
rs61995902	0.81[EUR][1000 genomes]
rs66533451	0.91[EUR][1000 genomes]
rs6714240	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6723195	0.91[EUR][1000 genomes]
rs67739992	0.91[EUR][1000 genomes]
rs67960524	0.89[EUR][1000 genomes]
rs68030749	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72618620	0.85[EUR][1000 genomes]
rs72618621	0.85[EUR][1000 genomes]
rs72618622	0.88[EUR][1000 genomes]
rs72618623	0.88[EUR][1000 genomes]
rs72618624	0.88[EUR][1000 genomes]
rs72618625	0.88[EUR][1000 genomes]
rs72618626	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72618627	0.88[EUR][1000 genomes]
rs72618628	0.88[AFR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72618629	0.88[AFR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72618631	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72618632	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72873772	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7573688	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7574467	0.88[EUR][1000 genomes]
rs7595513	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9710956	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[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	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
9	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
10	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
11	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
12	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
13	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
14	nsv581746	chr2:46699145-46719922	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46689200-46714800	Weak transcription	Right Atrium	heart
2	chr2:46700200-46714800	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr2:46704000-46705800	Enhancers	Primary T helper naive cells from peripheral blood	blood
4	chr2:46704200-46705400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr2:46704200-46705600	Enhancers	Primary T cells fromperipheralblood	blood
6	chr2:46704200-46705600	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr2:46704200-46705800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr2:46704400-46705200	Enhancers	Primary T killer memory cells from peripheral blood	blood
9	chr2:46704400-46705400	Enhancers	Fetal Thymus	thymus
10	chr2:46704400-46705600	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr2:46704400-46705600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
12	chr2:46704400-46705600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr2:46704400-46705800	Enhancers	H9 Cell Line	embryonic stem cell
14	chr2:46704400-46705800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr2:46704400-46706000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr2:46704800-46705400	Flanking Active TSS	K562	blood
17	chr2:46704800-46705600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr2:46705000-46705200	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr2:46705000-46705200	Enhancers	Primary T cells from cord blood	blood
20	chr2:46705000-46706000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
21	chr2:46705000-46707400	Weak transcription	Placenta	Placenta
22	chr2:46705000-46707600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr2:46705000-46716600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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