Variant report

Variant	rs3754466
Chromosome Location	chr1:158977947-158977948
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	STAT3	chr1:158977571-158977949	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr1:158977930-158978090	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:158900682..158902203-chr1:158976628..158979178,2	K562	blood:

Variant related genes	Relation type
IFI16	TF binding region
ENSG00000163564	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1102013	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1102014	0.95[ASN][1000 genomes]
rs1102015	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11590737	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs12239437	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1578477	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1614568	0.93[CHB][hapmap];0.92[ASN][1000 genomes]
rs1615480	1.00[CHB][hapmap];0.86[JPT][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1623601	1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs1772443	0.92[ASN][1000 genomes]
rs1935068	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1935070	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1935071	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2276404	0.86[JPT][hapmap]
rs2793856	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2793857	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3754464	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3754467	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41264051	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56954127	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57218670	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57498847	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58506115	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58805430	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60086314	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60381726	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61254442	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71632651	0.96[ASN][1000 genomes]
rs72480244	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72480246	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72480247	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72480248	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs856064	0.86[JPT][hapmap]
rs856125	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs856126	0.95[ASN][1000 genomes]
rs856127	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs856131	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs856132	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs856133	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs856134	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs856136	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs856140	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs860635	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3376764	chr1:158761947-158998617	Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	esv3369957	chr1:158915589-159003393	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
3	nsv3176	chr1:158955373-158986568	Flanking Active TSS Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:158969000-158978200	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr1:158970000-158978600	Weak transcription	Esophagus	oesophagus
3	chr1:158970200-158978600	Weak transcription	Psoas Muscle	Psoas
4	chr1:158970200-158978800	Weak transcription	Duodenum Mucosa	Duodenum
5	chr1:158970200-158979200	Weak transcription	Aorta	Aorta
6	chr1:158970800-158980800	Weak transcription	Pancreas	Pancrea
7	chr1:158971000-158978400	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr1:158971200-158978400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr1:158971200-158978400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:158971200-158978400	Weak transcription	HSMM	muscle
11	chr1:158971200-158978600	Weak transcription	Brain Angular Gyrus	brain
12	chr1:158971200-158978600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr1:158971200-158978800	Weak transcription	HSMMtube	muscle
14	chr1:158971400-158978400	Weak transcription	Hela-S3	cervix
15	chr1:158971800-158978600	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr1:158971800-158979800	Weak transcription	Colon Smooth Muscle	Colon
17	chr1:158972000-158979600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr1:158974800-158978400	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr1:158975000-158978800	Enhancers	Primary B cells from peripheral blood	blood
20	chr1:158975000-158979800	Weak transcription	Lung	lung
21	chr1:158975400-158978200	Weak transcription	Brain Cingulate Gyrus	brain
22	chr1:158975400-158978400	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr1:158975400-158978600	Enhancers	Primary hematopoietic stem cells	blood
24	chr1:158975400-158979200	Weak transcription	Liver	Liver
25	chr1:158975400-158979200	Weak transcription	Right Atrium	heart
26	chr1:158975600-158978200	Weak transcription	NHLF	lung
27	chr1:158975600-158978400	Weak transcription	Brain Anterior Caudate	brain
28	chr1:158975800-158978200	Weak transcription	Brain Substantia Nigra	brain
29	chr1:158975800-158978200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr1:158975800-158978400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr1:158975800-158978400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr1:158975800-158978400	Weak transcription	NHEK	skin
33	chr1:158975800-158978400	Weak transcription	Osteobl	bone
34	chr1:158975800-158978600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr1:158975800-158978600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr1:158975800-158978600	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr1:158975800-158979200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr1:158976000-158978200	Enhancers	Primary B cells from cord blood	blood
39	chr1:158976000-158978200	Weak transcription	Fetal Thymus	thymus
40	chr1:158976000-158978200	Weak transcription	NHDF-Ad	bronchial
41	chr1:158976000-158978400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr1:158976000-158978600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr1:158976000-158978600	Weak transcription	Adipose Nuclei	Adipose
44	chr1:158976000-158979000	Weak transcription	Fetal Stomach	stomach
45	chr1:158976000-158979200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr1:158976000-158979200	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr1:158976000-158979400	Weak transcription	Left Ventricle	heart
48	chr1:158976000-158979400	Weak transcription	Ovary	ovary
49	chr1:158976000-158979600	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr1:158976000-158983000	Weak transcription	Spleen	Spleen

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