Variant report

Variant	rs16850892
Chromosome Location	chr4:75172809-75172810
allele	G/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	CTCF	chr4:75172211-75172846	HCT-116	colon:	n/a	n/a
2	RAD21	chr4:75172226-75172829	HCT-116	colon:	n/a	n/a
3	RAD21	chr4:75172098-75172832	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:75167983..75171107-chr4:75171545..75173909,3	K562	blood:
2	chr4:75088731..75091267-chr4:75171967..75174863,2	K562	blood:
3	chr4:75172201..75173721-chr4:75181154..75183984,2	K562	blood:

Variant related genes	Relation type
EPGN	TF binding region
ENSG00000163738	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10006685	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10011730	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10014791	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10015148	0.90[ASN][1000 genomes]
rs1246576	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1246583	0.95[ASN][1000 genomes]
rs1246589	0.95[ASN][1000 genomes]
rs1246592	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1246593	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1246595	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1246596	0.95[ASN][1000 genomes]
rs1460004	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1542468	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs16850833	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16850864	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16850866	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16850885	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16850889	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16850898	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16850899	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16850903	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16850918	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16850929	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16850939	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2611754	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs28382340	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28417935	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28423375	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28434222	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28462312	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28588511	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28663170	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28721942	0.82[ASN][1000 genomes]
rs28788278	0.90[ASN][1000 genomes]
rs492042	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs56667969	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs572987	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs579866	1.00[CEU][hapmap]
rs6821364	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6845763	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs734222	1.00[CEU][hapmap]
rs7656041	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7656313	0.90[ASN][1000 genomes]
rs7665228	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7670644	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7689369	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7694828	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7697394	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9683437	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9884572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9884653	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9992624	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9993008	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525980	chr4:74731526-75382209	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1009099	chr4:75089233-75726206	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:75134000-75173800	Weak transcription	Primary T cells from cord blood	blood
2	chr4:75149800-75186200	Weak transcription	K562	blood
3	chr4:75156600-75174200	Weak transcription	Primary hematopoietic stem cells	blood
4	chr4:75160200-75173800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr4:75163600-75173200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr4:75171400-75173800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr4:75171800-75174000	Enhancers	Hela-S3	cervix
8	chr4:75172000-75173000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr4:75172000-75173600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr4:75172200-75173800	Enhancers	NHEK	skin
11	chr4:75172600-75173800	Enhancers	HMEC	breast
12	chr4:75172800-75173000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr4:75172800-75173800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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