Variant report

Variant	rs6850509
Chromosome Location	chr4:88226572-88226573
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	STAT3	chr4:88225826-88226610	Hela-S3	cervix:	n/a	n/a
2	FOXM1	chr4:88225661-88226647	MCF-7	breast:	n/a	n/a
3	GATA3	chr4:88225620-88226575	MCF-7	breast:	n/a	n/a
4	GATA3	chr4:88225597-88226753	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:88226132..88228278-chr4:88229243..88230944,2	MCF-7	breast:
2	chr4:88224415..88227242-chr4:88231505..88233396,2	K562	blood:
3	chr4:88225790..88227669-chr4:88236912..88239118,2	MCF-7	breast:
4	chr4:88225793..88228433-chr4:88233021..88235909,2	MCF-7	breast:

Variant related genes	Relation type
MIR5705	TF binding region

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10001545	0.88[ASN][1000 genomes]
rs10022237	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10084835	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10433879	0.92[ASN][1000 genomes]
rs10433937	0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10440365	0.94[ASN][1000 genomes]
rs11727374	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11735092	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11935592	0.88[ASN][1000 genomes]
rs13130041	0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs13130929	0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs13140105	0.93[ASN][1000 genomes]
rs13142110	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13142655	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13150068	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13150834	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28418877	0.88[ASN][1000 genomes]
rs28419230	0.89[ASN][1000 genomes]
rs28439498	0.87[ASN][1000 genomes]
rs28456144	0.95[ASN][1000 genomes]
rs28528308	0.94[ASN][1000 genomes]
rs28636836	0.87[ASN][1000 genomes]
rs28657030	0.94[ASN][1000 genomes]
rs28664118	0.88[ASN][1000 genomes]
rs28679728	0.88[ASN][1000 genomes]
rs4089	0.95[ASN][1000 genomes]
rs4998663	0.88[ASN][1000 genomes]
rs6531967	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6834488	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6850131	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs7663544	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7684895	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7694379	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997750	chr4:87933945-88264127	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1007020	chr4:88046263-88235018	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv537169	chr4:88046263-88235018	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv516203	chr4:88167878-88228228	Enhancers Strong transcription Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
5	nsv870296	chr4:88173534-88295927	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv470050	chr4:88186509-88228228	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
7	esv2760913	chr4:88194170-88228412	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
8	nsv879527	chr4:88194170-88250203	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
9	esv1802846	chr4:88211056-88246450	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1004518	chr4:88218473-88354403	Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:88225400-88237800	Strong transcription	Liver	Liver
2	chr4:88225800-88227200	Active TSS	Hela-S3	cervix
3	chr4:88226000-88226600	Active TSS	A549	lung
4	chr4:88226200-88226600	Active TSS	Aorta	Aorta
5	chr4:88226200-88226800	Active TSS	NHEK	skin
6	chr4:88226400-88231600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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