Variant report

Variant	rs12190509
Chromosome Location	chr6:74776402-74776403
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	FOS	chr6:74775893-74776479	MCF10A-Er-Src	breast:	n/a	chr6:74776051-74776062
2	CTCF	chr6:74776260-74776410	HMEC	breast:	n/a	n/a
3	CTCF	chr6:74776260-74776410	SAEC	small airway:	n/a	n/a
4	FOS	chr6:74775867-74776504	MCF10A-Er-Src	breast:	n/a	chr6:74776051-74776062
5	FOS	chr6:74775890-74776512	MCF10A-Er-Src	breast:	n/a	chr6:74776051-74776062
6	CTCF	chr6:74776260-74776410	HEEpiC	esophagus:	n/a	n/a
7	MYC	chr6:74776033-74776505	MCF10A-Er-Src	breast:	n/a	n/a
8	STAT3	chr6:74776126-74776505	MCF10A-Er-Src	breast:	n/a	chr6:74776172-74776183
9	STAT3	chr6:74776260-74776559	MCF10A-Er-Src	breast:	n/a	n/a
10	STAT3	chr6:74775863-74776509	MCF10A-Er-Src	breast:	n/a	chr6:74776172-74776183 chr6:74775979-74775987
11	CEBPB	chr6:74775980-74776424	IMR90	lung:	n/a	n/a
12	FOS	chr6:74775867-74776483	MCF10A-Er-Src	breast:	n/a	chr6:74776051-74776062
13	STAT3	chr6:74776146-74776575	MCF10A-Er-Src	breast:	n/a	chr6:74776172-74776183

Variant related genes	Relation type
ENSG00000223786	TF binding region

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10485388	0.99[EUR][1000 genomes]
rs11751061	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11751175	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11751771	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs11754164	0.91[EUR][1000 genomes]
rs11756254	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11757198	0.94[EUR][1000 genomes]
rs11757917	0.80[EUR][1000 genomes]
rs12191462	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12191866	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12193999	0.95[EUR][1000 genomes]
rs12198091	0.97[EUR][1000 genomes]
rs12202104	1.00[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs12202674	0.93[EUR][1000 genomes]
rs12205582	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12205749	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12206043	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12209564	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12209571	0.99[EUR][1000 genomes]
rs12213297	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12213804	0.83[EUR][1000 genomes]
rs12215639	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3923228	0.98[EUR][1000 genomes]
rs4279396	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4501395	0.91[ASN][1000 genomes]
rs4537105	0.95[EUR][1000 genomes]
rs4546447	1.00[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs4644011	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55789428	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56104278	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56138029	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs56343698	0.87[ASN][1000 genomes]
rs56362119	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs56396434	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66472340	1.00[EUR][1000 genomes]
rs66865230	1.00[EUR][1000 genomes]
rs72952371	1.00[EUR][1000 genomes]
rs72952395	0.97[EUR][1000 genomes]
rs72952398	0.98[EUR][1000 genomes]
rs72955114	0.91[ASN][1000 genomes]
rs72955123	0.91[ASN][1000 genomes]
rs72955171	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72955173	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72955185	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72955196	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72955199	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72955201	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72962230	0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030389	chr6:74606701-74811706	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	esv3394316	chr6:74630005-74935625	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv603733	chr6:74666559-74944460	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	esv3327625	chr6:74716120-74971605	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	esv3440413	chr6:74741688-74791357	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv886161	chr6:74765488-74800529	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:74775000-74776600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr6:74775400-74776600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr6:74775600-74776600	Enhancers	Osteobl	bone
4	chr6:74775800-74776600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr6:74775800-74776600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:74775800-74776600	Enhancers	Muscle Satellite Cultured Cells	--
7	chr6:74775800-74776600	Enhancers	NHDF-Ad	bronchial
8	chr6:74775800-74776800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr6:74776000-74776600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr6:74776000-74776600	Flanking Active TSS	NHEK	skin
11	chr6:74776200-74776600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr6:74776200-74776600	Enhancers	HSMM	muscle
13	chr6:74776400-74776600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr6:74776400-74776800	Enhancers	HMEC	breast
15	chr6:74776400-74778600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr6:74776400-74778800	Weak transcription	Fetal Muscle Leg	muscle
17	chr6:74776400-74783000	Weak transcription	NH-A	brain

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