Variant report

Variant	rs1720041
Chromosome Location	chr12:122457579-122457580
allele	A/C
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	POLR2A	chr12:122457262-122457728	Raji	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:122236783..122240484-chr12:122457021..122461932,5	MCF-7	breast:
2	chr12:122455179..122457672-chr12:122458203..122460208,2	MCF-7	breast:
3	chr12:122354300..122356847-chr12:122457161..122460061,2	K562	blood:
4	chr12:122236856..122239163-chr12:122456320..122458969,2	K562	blood:

Variant related genes	Relation type
BCL7A	TF binding region
ENSG00000212694	Chromatin interaction
ENSG00000158023	Chromatin interaction
ENSG00000139725	Chromatin interaction
ENSG00000110987	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11043248	0.81[LWK][hapmap]
rs1154510	0.82[CEU][hapmap];0.84[LWK][hapmap];0.85[MEX][hapmap]
rs1154513	0.82[AMR][1000 genomes]
rs1169075	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs1169077	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1169080	0.87[AMR][1000 genomes]
rs1169082	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1169085	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.97[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1169092	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1169093	1.00[ASW][hapmap];1.00[CEU][hapmap];0.80[CHB][hapmap];0.97[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1182927	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1185260	0.82[CEU][hapmap];0.81[CHB][hapmap];0.81[GIH][hapmap];0.82[AMR][1000 genomes]
rs1667580	0.81[AMR][1000 genomes]
rs1667583	0.82[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];0.81[GIH][hapmap];0.90[MEX][hapmap]
rs1667584	0.82[AMR][1000 genomes]
rs1678951	0.81[AMR][1000 genomes]
rs1678969	0.87[CHB][hapmap]
rs1916333	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2230681	0.82[CEU][hapmap]
rs2247291	0.82[CEU][hapmap]
rs2596144	0.82[CEU][hapmap]
rs2620340	0.82[CEU][hapmap]
rs2707056	0.82[CEU][hapmap]
rs4760099	0.82[CEU][hapmap]
rs493519	0.82[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];0.81[GIH][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.82[YRI][hapmap];0.86[AMR][1000 genomes]
rs529736	0.86[MEX][hapmap]
rs6486794	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs693277	0.82[AMR][1000 genomes]
rs7314056	0.82[CEU][hapmap];0.85[MEX][hapmap]
rs7957207	1.00[ASW][hapmap];0.91[CEU][hapmap];0.94[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7961103	1.00[ASW][hapmap];0.91[CEU][hapmap];0.94[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs830116	0.82[AMR][1000 genomes]
rs830120	0.90[MEX][hapmap]
rs830122	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs830123	1.00[MEX][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes]
rs830124	0.82[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap]
rs830126	0.86[AMR][1000 genomes]
rs853758	0.82[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes]
rs895958	0.82[CEU][hapmap];0.81[CHB][hapmap];0.81[GIH][hapmap];0.81[LWK][hapmap];0.90[MEX][hapmap];0.81[AMR][1000 genomes]
rs895959	0.82[CEU][hapmap]
rs9739533	0.90[AMR][1000 genomes];0.83[EUR][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	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
2	nsv916686	chr12:122240149-122714056	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	esv34001	chr12:122298737-122521637	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats 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	35 gene(s)	inside rSNPs	diseases
4	esv3338715	chr12:122457569-122462467	Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122442600-122458800	Weak transcription	Aorta	Aorta
2	chr12:122443000-122458800	Weak transcription	Brain Anterior Caudate	brain
3	chr12:122443400-122458800	Weak transcription	Right Ventricle	heart
4	chr12:122443400-122459000	Weak transcription	Right Atrium	heart
5	chr12:122444600-122458600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr12:122454800-122459000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr12:122455600-122458800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr12:122456000-122457600	ZNF genes & repeats	Fetal Thymus	thymus
9	chr12:122456000-122457600	Enhancers	Dnd41	blood
10	chr12:122456400-122458800	Weak transcription	Pancreas	Pancrea
11	chr12:122456600-122458600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr12:122456800-122458800	Enhancers	Primary B cells from peripheral blood	blood
13	chr12:122457000-122458600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr12:122457400-122457600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
15	chr12:122457400-122457600	Enhancers	Thymus	Thymus
16	chr12:122457400-122457800	ZNF genes & repeats	K562	blood

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