Variant report

Variant	rs4946406
Chromosome Location	chr6:119594032-119594033
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	POLR2A	chr6:119593866-119595281	K562	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000216316	TF binding region

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11153802	0.83[AFR][1000 genomes]
rs11962211	0.87[YRI][hapmap]
rs12209570	0.91[CHB][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs12215906	0.94[ASN][1000 genomes]
rs1295391	0.89[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap]
rs1295392	0.86[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap]
rs1324554	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1408492	0.88[AFR][1000 genomes]
rs1408493	0.88[AFR][1000 genomes]
rs195046	0.84[YRI][hapmap]
rs195048	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs195056	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs195058	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs195090	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs195091	0.86[YRI][hapmap]
rs195092	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2057554	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2267673	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2267674	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2267675	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2267676	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2299878	1.00[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2299886	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2357164	1.00[CEU][hapmap];0.82[JPT][hapmap];0.91[YRI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3778111	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3819731	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6569074	0.87[YRI][hapmap]
rs6937640	0.85[EUR][1000 genomes]
rs7755155	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7755572	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9320684	0.84[YRI][hapmap]
rs9489630	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9489638	1.00[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs975578	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025995	chr6:119407742-119709548	Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv886570	chr6:119450888-119600556	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv1017507	chr6:119465981-119664949	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	esv3447598	chr6:119558591-120119384	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	esv3389526	chr6:119558598-120190087	ZNF genes & repeats Enhancers Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:119558800-119602000	Weak transcription	Gastric	stomach
2	chr6:119589200-119598600	Weak transcription	Colon Smooth Muscle	Colon
3	chr6:119589200-119611000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr6:119590600-119621800	Weak transcription	Placenta	Placenta
5	chr6:119590800-119617400	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr6:119590800-119626600	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr6:119591000-119599800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:119591000-119599800	Weak transcription	Lung	lung
9	chr6:119591000-119600600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr6:119591000-119624200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr6:119591200-119602000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr6:119591200-119604600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr6:119591400-119601400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr6:119591600-119595200	ZNF genes & repeats	K562	blood
15	chr6:119591800-119597000	Weak transcription	Fetal Kidney	kidney
16	chr6:119592000-119594200	ZNF genes & repeats	HepG2	liver
17	chr6:119592000-119602200	Weak transcription	Left Ventricle	heart
18	chr6:119592000-119604200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr6:119592200-119594600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr6:119592200-119594600	Weak transcription	NHDF-Ad	bronchial
21	chr6:119592200-119597400	Weak transcription	NHLF	lung
22	chr6:119592200-119622200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr6:119592400-119594600	Weak transcription	Adipose Nuclei	Adipose
24	chr6:119592400-119596800	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr6:119592400-119597200	Weak transcription	Liver	Liver
26	chr6:119592400-119601200	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr6:119592400-119604800	Weak transcription	Fetal Intestine Large	intestine
28	chr6:119592400-119610600	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr6:119592400-119620800	Weak transcription	Duodenum Mucosa	Duodenum
30	chr6:119592400-119633600	Weak transcription	Primary T cells from cord blood	blood
31	chr6:119592600-119594400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr6:119592600-119622200	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr6:119592600-119627200	Weak transcription	Dnd41	blood
34	chr6:119592800-119594200	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr6:119593000-119599800	Weak transcription	Aorta	Aorta
36	chr6:119593000-119622200	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr6:119593000-119624800	Weak transcription	Fetal Thymus	thymus
38	chr6:119593000-119626800	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr6:119593200-119594600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr6:119593200-119604600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr6:119593400-119595000	Enhancers	Fetal Lung	lung
42	chr6:119593400-119595600	Strong transcription	Primary hematopoietic stem cells	blood
43	chr6:119593600-119594800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr6:119593600-119596800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr6:119593800-119596800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr6:119593800-119597000	Weak transcription	Primary B cells from cord blood	blood
47	chr6:119594000-119596000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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