Variant report

Variant	rs4682298
Chromosome Location	chr3:111447059-111447060
allele	A/G
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	MAFF	chr3:111446753-111447090	HepG2	liver:	n/a	chr3:111446901-111446919
2	RAD21	chr3:111446955-111447368	H1-hESC	embryonic stem cell:	n/a	n/a
3	MAFK	chr3:111446733-111447096	HepG2	liver:	n/a	n/a
4	CTCF	chr3:111447040-111447190	HRE	kidney:	n/a	chr3:111447177-111447190
5	MAFK	chr3:111446757-111447089	IMR90	lung:	n/a	n/a
6	RAD21	chr3:111446979-111447324	HepG2	liver:	n/a	n/a
7	MAFK	chr3:111446762-111447094	HepG2	liver:	n/a	n/a
8	POLR2A	chr3:111446572-111447328	A549	lung:	n/a	n/a
9	RAD21	chr3:111447013-111447433	HCT-116	colon:	n/a	n/a

Variant related genes	Relation type
PLCXD2	TF binding region
PHLDB2	TF binding region

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1105448	0.82[JPT][hapmap]
rs11711533	0.82[CHB][hapmap]
rs11711582	0.91[ASW][hapmap];0.82[CHB][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs12330761	0.82[CEU][hapmap];0.80[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs12494734	0.82[JPT][hapmap]
rs1398751	0.86[JPT][hapmap]
rs1398753	0.86[JPT][hapmap]
rs1398754	0.86[JPT][hapmap]
rs2137595	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2292518	0.86[JPT][hapmap]
rs2399394	0.86[JPT][hapmap]
rs4401340	0.82[JPT][hapmap];0.84[TSI][hapmap]
rs4413291	0.91[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.88[MKK][hapmap];0.91[TSI][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4414820	0.86[JPT][hapmap]
rs4682054	0.82[ASW][hapmap]
rs4682057	0.80[AFR][1000 genomes]
rs4682299	0.91[ASW][hapmap];0.82[CEU][hapmap];0.82[CHB][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs4682303	0.82[CEU][hapmap];0.80[EUR][1000 genomes]
rs56028731	0.81[EUR][1000 genomes]
rs62275532	0.81[EUR][1000 genomes]
rs6784753	0.91[ASW][hapmap];0.82[CEU][hapmap];0.89[TSI][hapmap]
rs6788543	0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs6796087	0.89[TSI][hapmap]
rs7646161	0.82[JPT][hapmap]
rs7646453	0.82[JPT][hapmap]
rs882591	0.86[JPT][hapmap]
rs955381	0.81[EUR][1000 genomes]
rs959540	0.81[EUR][1000 genomes]
rs9854875	0.86[JPT][hapmap]
rs9868909	0.82[CEU][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs9877859	0.83[ASW][hapmap];0.85[CEU][hapmap]

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	nsv460821	chr3:110637471-111501097	Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv591275	chr3:110637471-111501097	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv591290	chr3:111427455-111462570	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111415200-111454200	Weak transcription	Small Intestine	intestine
2	chr3:111420400-111450600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr3:111427200-111448400	Weak transcription	Right Ventricle	heart
4	chr3:111427600-111456000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr3:111428800-111451200	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr3:111431600-111451400	Weak transcription	Gastric	stomach
7	chr3:111432000-111448400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr3:111432000-111448600	Weak transcription	Brain Germinal Matrix	brain
9	chr3:111434000-111451200	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr3:111435200-111447800	Weak transcription	HUVEC	blood vessel
11	chr3:111436800-111448400	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr3:111440400-111448400	Weak transcription	Right Atrium	heart
13	chr3:111440800-111451200	Weak transcription	Primary B cells from cord blood	blood
14	chr3:111441400-111448400	Weak transcription	Fetal Muscle Leg	muscle
15	chr3:111441400-111451000	Weak transcription	Fetal Intestine Small	intestine
16	chr3:111441600-111449800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr3:111441600-111452800	Weak transcription	Placenta	Placenta
18	chr3:111442000-111450000	Weak transcription	Thymus	Thymus
19	chr3:111442000-111452000	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr3:111442000-111454200	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr3:111442400-111456000	Weak transcription	Lung	lung
22	chr3:111442600-111448400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr3:111442600-111451200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr3:111442800-111447200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr3:111442800-111447200	Weak transcription	NHEK	skin
26	chr3:111442800-111448000	Weak transcription	Hela-S3	cervix
27	chr3:111442800-111448200	Weak transcription	Adipose Nuclei	Adipose
28	chr3:111442800-111448400	Weak transcription	Fetal Stomach	stomach
29	chr3:111442800-111455800	Weak transcription	Rectal Smooth Muscle	rectum
30	chr3:111443000-111447200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr3:111443000-111447400	Weak transcription	HMEC	breast
32	chr3:111443000-111447400	Weak transcription	HSMM	muscle
33	chr3:111443000-111448000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr3:111443000-111448400	Weak transcription	Left Ventricle	heart
35	chr3:111443000-111448400	Weak transcription	Ovary	ovary
36	chr3:111443000-111448400	Weak transcription	A549	lung
37	chr3:111443200-111448000	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr3:111443200-111448000	Weak transcription	NHDF-Ad	bronchial
39	chr3:111443200-111448200	Weak transcription	NHLF	lung
40	chr3:111443200-111454800	Weak transcription	Primary T cells from cord blood	blood
41	chr3:111443400-111448000	Weak transcription	Osteobl	bone
42	chr3:111443400-111448400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr3:111443600-111448000	Weak transcription	HSMMtube	muscle
44	chr3:111443800-111448000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr3:111443800-111448200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr3:111443800-111448400	Weak transcription	Esophagus	oesophagus
47	chr3:111443800-111451400	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr3:111444000-111448400	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr3:111444200-111456000	Weak transcription	Aorta	Aorta
50	chr3:111444800-111449200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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