Variant report

Variant	rs62406694
Chromosome Location	chr5:179102918-179102919
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:15 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:179102066-179104449	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr5:179101513-179106171	HepG2	liver:	n/a	n/a
3	POLR2A	chr5:179102753-179102995	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr5:179102741-179103634	K562	blood:	n/a	n/a
5	POLR2A	chr5:179102757-179102987	K562	blood:	n/a	n/a
6	POLR2A	chr5:179102712-179104243	K562	blood:	n/a	n/a
7	TBP	chr5:179102696-179103033	K562	blood:	n/a	n/a
8	POLR2A	chr5:179102755-179103308	HCT-116	colon:	n/a	n/a
9	POLR2A	chr5:179102776-179103382	HepG2	liver:	n/a	n/a
10	POLR2A	chr5:179102687-179103020	K562	blood:	n/a	n/a
11	POLR2A	chr5:179102883-179103270	GM12878	blood:	n/a	n/a
12	POLR2A	chr5:179102775-179103000	ECC-1	luminal epithelium:	n/a	n/a
13	POLR2A	chr5:179102689-179104345	HepG2	liver:	n/a	n/a
14	POLR2A	chr5:179101705-179104250	K562	blood:	n/a	n/a
15	POLR2A	chr5:179102021-179104393	SK-N-MC	brain:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:179101962..179108661-chr5:179122383..179128408,19	MCF-7	breast:
2	chr5:179100838..179108153-chr5:179124449..179130181,22	K562	blood:
3	chr5:179101603..179111989-chr5:179122927..179129527,32	MCF-7	breast:
4	chr5:179100989..179111182-chr5:179122076..179128627,19	K562	blood:
5	chr5:179047581..179051358-chr5:179102429..179108878,16	K562	blood:
6	chr5:179102368..179107935-chr5:179157286..179161555,5	K562	blood:
7	chr5:179048811..179053260-chr5:179101652..179108160,8	MCF-7	breast:
8	chr5:179032616..179037685-chr5:179101606..179106447,5	K562	blood:
9	chr5:179038238..179040444-chr5:179101128..179103965,2	K562	blood:
10	chr5:179102777..179105502-chr5:179129566..179131277,2	MCF-7	breast:

No data

Variant related genes	Relation type
HMGB3P22	TF binding region
CANX	TF binding region
ENSG00000161021	Chromatin interaction
ENSG00000127022	Chromatin interaction
ENSG00000176783	Chromatin interaction
ENSG00000169045	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11749841	0.83[ASN][1000 genomes]
rs4388174	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4701195	0.82[ASN][1000 genomes]
rs57551480	0.82[ASN][1000 genomes]
rs62406695	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6601065	0.85[ASN][1000 genomes]
rs72662129	0.87[ASN][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	nsv949554	chr5:178832325-179309513	Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
2	nsv883270	chr5:178951106-179350387	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
3	nsv830560	chr5:179039212-179175758	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
4	nsv1021275	chr5:179056475-179104588	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv1031352	chr5:179082461-179104588	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv1023502	chr5:179086091-179105316	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179085800-179103800	Weak transcription	GM12878-XiMat	blood
2	chr5:179085800-179104000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr5:179085800-179104200	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr5:179085800-179104200	Weak transcription	A549	lung
5	chr5:179085800-179104600	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr5:179085800-179104600	Weak transcription	Brain Hippocampus Middle	brain
7	chr5:179085800-179104600	Weak transcription	Esophagus	oesophagus
8	chr5:179085800-179104600	Weak transcription	Fetal Kidney	kidney
9	chr5:179085800-179104800	Weak transcription	Right Ventricle	heart
10	chr5:179085800-179105000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr5:179086000-179103600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr5:179086000-179104000	Weak transcription	Fetal Brain Male	brain
13	chr5:179086000-179104400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr5:179086000-179104600	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr5:179086000-179104600	Weak transcription	NHEK	skin
16	chr5:179086200-179104200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr5:179086200-179104600	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr5:179086200-179104800	Weak transcription	Brain Angular Gyrus	brain
19	chr5:179091000-179104600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr5:179091600-179103800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr5:179091800-179104800	Weak transcription	Ovary	ovary
22	chr5:179091800-179104800	Weak transcription	NHLF	lung
23	chr5:179092200-179105000	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr5:179092400-179104000	Weak transcription	Liver	Liver
25	chr5:179092400-179104400	Weak transcription	Brain Cingulate Gyrus	brain
26	chr5:179092400-179104600	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr5:179092600-179103000	Weak transcription	HepG2	liver
28	chr5:179092600-179103600	Weak transcription	Pancreas	Pancrea
29	chr5:179092600-179103800	Weak transcription	Dnd41	blood
30	chr5:179092600-179104200	Weak transcription	Osteobl	bone
31	chr5:179092600-179104600	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr5:179092600-179104600	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr5:179092600-179104800	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr5:179092800-179104400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr5:179092800-179104400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr5:179092800-179105000	Weak transcription	Left Ventricle	heart
37	chr5:179093000-179103600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr5:179093000-179104000	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr5:179093000-179104000	Weak transcription	Thymus	Thymus
40	chr5:179093000-179104200	Weak transcription	Colon Smooth Muscle	Colon
41	chr5:179093000-179104600	Weak transcription	Adipose Nuclei	Adipose
42	chr5:179093000-179104800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr5:179093000-179105000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr5:179093200-179104000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr5:179093200-179104400	Weak transcription	Spleen	Spleen
46	chr5:179093200-179104600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr5:179093400-179103400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr5:179093400-179103600	Weak transcription	Fetal Intestine Large	intestine
49	chr5:179093400-179104000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr5:179093400-179104000	Weak transcription	Lung	lung

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