Variant report

Variant	rs17206564
Chromosome Location	chr12:10464017-10464018
allele	A/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	FOS	chr12:10463916-10464419	MCF10A-Er-Src	breast:	n/a	chr12:10464384-10464393
2	STAT3	chr12:10463993-10464355	Hela-S3	cervix:	n/a	n/a
3	STAT3	chr12:10463993-10464249	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr12:10463884-10464294	MCF10A-Er-Src	breast:	n/a	n/a
5	STAT3	chr12:10463935-10464126	MCF10A-Er-Src	breast:	n/a	n/a
6	STAT3	chr12:10463938-10464324	MCF10A-Er-Src	breast:	n/a	n/a
7	STAT3	chr12:10463974-10464361	MCF10A-Er-Src	breast:	n/a	n/a
8	MYC	chr12:10464013-10464330	MCF10A-Er-Src	breast:	n/a	n/a
9	CEBPB	chr12:10463938-10464283	Hela-S3	cervix:	n/a	n/a
10	MYC	chr12:10463919-10464240	MCF10A-Er-Src	breast:	n/a	n/a
11	GATA2	chr12:10463525-10464275	HUVEC	blood vessel:	n/a	n/a
12	FOS	chr12:10463434-10464398	HUVEC	blood vessel:	n/a	chr12:10464384-10464393
13	FOS	chr12:10463932-10464249	MCF10A-Er-Src	breast:	n/a	n/a
14	FOS	chr12:10463887-10464398	MCF10A-Er-Src	breast:	n/a	chr12:10464384-10464393

Variant related genes	Relation type
KLRD1	TF binding region

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10743881	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10845099	0.94[TSI][hapmap]
rs10845104	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11053701	0.80[ASN][1000 genomes]
rs11053722	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs11612335	0.93[ASN][1000 genomes]
rs11830137	0.82[CEU][hapmap]
rs12302171	0.83[AMR][1000 genomes]
rs12303774	0.80[ASN][1000 genomes]
rs12304713	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12311695	0.91[EUR][1000 genomes]
rs12315681	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12315815	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12813575	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12814085	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12817905	0.88[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12818742	0.83[AMR][1000 genomes]
rs12821332	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12824930	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12828163	0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12828540	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12829898	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12831232	0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12832221	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12832489	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2537765	0.88[ASN][1000 genomes]
rs2537793	1.00[CEU][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2537805	0.85[ASN][1000 genomes]
rs2617128	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2617135	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes]
rs2617137	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs2927558	0.90[EUR][1000 genomes]
rs34282122	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34790670	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34859528	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34956502	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35510688	0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs35518026	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35868193	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4254156	0.83[TSI][hapmap]
rs4346056	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4365134	0.83[AMR][1000 genomes]
rs4764331	0.83[TSI][hapmap]
rs4764369	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes]
rs56272210	0.92[ASN][1000 genomes]
rs58700703	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6488275	0.87[CEU][hapmap]
rs7136409	0.94[TSI][hapmap]
rs71450033	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71450034	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs765790	0.94[TSI][hapmap]
rs765792	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7958472	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes]
rs7963011	0.80[ASN][1000 genomes]
rs7969664	0.84[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	nsv898757	chr12:10229281-10614641	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv832328	chr12:10398071-10620443	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv605	chr12:10448638-10494208	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv898759	chr12:10454556-10583365	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17206564	RP11-656E20.5	cis	Muscle Skeletal	GTEx

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:10454800-10474400	Weak transcription	Left Ventricle	heart
2	chr12:10458000-10464200	Active TSS	Primary T cells fromperipheralblood	blood
3	chr12:10461200-10467400	Transcr. at gene 5' and 3'	Primary Natural Killer cells fromperipheralblood	blood
4	chr12:10462800-10471400	Weak transcription	Right Ventricle	heart
5	chr12:10463200-10470800	Weak transcription	Placenta	Placenta
6	chr12:10463400-10464400	Enhancers	Muscle Satellite Cultured Cells	--
7	chr12:10463400-10464400	Flanking Active TSS	HUVEC	blood vessel
8	chr12:10463600-10464400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr12:10463600-10464400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr12:10463800-10464400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr12:10463800-10464400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr12:10463800-10470600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr12:10464000-10464400	Flanking Active TSS	Hela-S3	cervix
14	chr12:10464000-10464600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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