Variant report

Variant	rs10063009
Chromosome Location	chr5:179104218-179104219
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 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	chr5:179103510-179104360	K562	blood:	n/a	n/a
3	POLR2A	chr5:179101513-179106171	HepG2	liver:	n/a	n/a
4	POLR2A	chr5:179103645-179104232	K562	blood:	n/a	n/a
5	POLR2A	chr5:179102712-179104243	K562	blood:	n/a	n/a
6	POLR2A	chr5:179103389-179104682	K562	blood:	n/a	n/a
7	MAX	chr5:179103955-179104345	K562	blood:	n/a	n/a
8	POLR2A	chr5:179104166-179104223	GM12878	blood:	n/a	n/a
9	POLR2A	chr5:179102689-179104345	HepG2	liver:	n/a	n/a
10	POLR2A	chr5:179101705-179104250	K562	blood:	n/a	n/a
11	POLR2A	chr5:179102021-179104393	SK-N-MC	brain:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr5:179101962..179108661-chr5:179122383..179128408,19	MCF-7	breast:
2	chr5:179104081..179106481-chr5:179247871..179249548,2	K562	blood:
3	chr5:179100838..179108153-chr5:179124449..179130181,22	K562	blood:
4	chr5:179104047..179107935-chr5:179157751..179161258,3	K562	blood:
5	chr5:179104105..179106791-chr5:179194829..179197317,2	K562	blood:
6	chr5:179101603..179111989-chr5:179122927..179129527,32	MCF-7	breast:
7	chr5:179100989..179111182-chr5:179122076..179128627,19	K562	blood:
8	chr5:179047581..179051358-chr5:179102429..179108878,16	K562	blood:
9	chr5:179102368..179107935-chr5:179157286..179161555,5	K562	blood:
10	chr5:179104067..179106595-chr5:179220718..179223236,3	MCF-7	breast:
11	chr5:179048811..179053260-chr5:179101652..179108160,8	MCF-7	breast:
12	chr5:179104088..179107429-chr5:179222108..179224529,3	MCF-7	breast:
13	chr5:179048156..179052144-chr5:179103013..179109071,12	K562	blood:
14	chr5:178986726..178988892-chr5:179104044..179106638,2	K562	blood:
15	chr5:179032616..179037685-chr5:179101606..179106447,5	K562	blood:
16	chr5:179103716..179105834-chr5:179232132..179234075,2	MCF-7	breast:
17	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
ENSG00000161011	Chromatin interaction
ENSG00000169045	Chromatin interaction
ENSG00000161013	Chromatin interaction
ENSG00000127022	Chromatin interaction
ENSG00000213316	Chromatin interaction
ENSG00000176783	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs10053812	1.00[AFR][1000 genomes]
rs9329088	0.81[AFR][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:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179085800-179104600	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr5:179085800-179104600	Weak transcription	Brain Hippocampus Middle	brain
3	chr5:179085800-179104600	Weak transcription	Esophagus	oesophagus
4	chr5:179085800-179104600	Weak transcription	Fetal Kidney	kidney
5	chr5:179085800-179104800	Weak transcription	Right Ventricle	heart
6	chr5:179085800-179105000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr5:179086000-179104400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr5:179086000-179104600	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr5:179086000-179104600	Weak transcription	NHEK	skin
10	chr5:179086200-179104600	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr5:179086200-179104800	Weak transcription	Brain Angular Gyrus	brain
12	chr5:179091000-179104600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr5:179091800-179104800	Weak transcription	Ovary	ovary
14	chr5:179091800-179104800	Weak transcription	NHLF	lung
15	chr5:179092200-179105000	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr5:179092400-179104400	Weak transcription	Brain Cingulate Gyrus	brain
17	chr5:179092400-179104600	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr5:179092600-179104600	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr5:179092600-179104600	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr5:179092600-179104800	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr5:179092800-179104400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr5:179092800-179104400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr5:179092800-179105000	Weak transcription	Left Ventricle	heart
24	chr5:179093000-179104600	Weak transcription	Adipose Nuclei	Adipose
25	chr5:179093000-179104800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr5:179093000-179105000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr5:179093200-179104400	Weak transcription	Spleen	Spleen
28	chr5:179093200-179104600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr5:179093400-179104400	Weak transcription	Fetal Intestine Small	intestine
30	chr5:179093400-179104600	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr5:179093400-179104600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr5:179093400-179104600	Weak transcription	Brain Anterior Caudate	brain
33	chr5:179093400-179104600	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr5:179093400-179104600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr5:179093400-179104800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr5:179093600-179104800	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr5:179095800-179104600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr5:179097000-179104400	Weak transcription	Duodenum Mucosa	Duodenum
39	chr5:179097000-179104600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr5:179097000-179104600	Weak transcription	Stomach Smooth Muscle	stomach
41	chr5:179097200-179104600	Weak transcription	Fetal Brain Female	brain
42	chr5:179098200-179104800	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr5:179102400-179104400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr5:179102400-179104600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr5:179102400-179104800	Weak transcription	Fetal Lung	lung
46	chr5:179103200-179104600	Enhancers	Primary T cells fromperipheralblood	blood
47	chr5:179103400-179104800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr5:179103600-179104400	Flanking Active TSS	HepG2	liver
49	chr5:179103600-179104600	Enhancers	Fetal Intestine Large	intestine
50	chr5:179103600-179104800	Enhancers	Pancreas	Pancrea

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links