Variant report

Variant	rs10913708
Chromosome Location	chr1:179264397-179264398
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:179263909..179265943-chr1:179276676..179278197,2	MCF-7	breast:
2	chr1:179260885..179265137-chr1:179333383..179339387,7	MCF-7	breast:
3	chr1:179050855..179052664-chr1:179261724..179264711,2	K562	blood:
4	chr1:179050855..179053575-chr1:179263211..179266215,3	K562	blood:
5	chr1:179110656..179113275-chr1:179262488..179264481,2	K562	blood:

Variant related genes	Relation type
ENSG00000143322	Chromatin interaction
ENSG00000263633	Chromatin interaction
ENSG00000186283	Chromatin interaction
ENSG00000162779	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10798660	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10913692	0.82[CHD][hapmap]
rs10913710	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10913711	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10913712	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10913720	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10913721	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10913722	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10913724	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10913725	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10913727	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11545566	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11576517	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap];0.90[ASN][1000 genomes]
rs11589635	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11806924	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11810201	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12023125	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12026841	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12031660	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12038140	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12038774	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12039261	0.91[ASN][1000 genomes]
rs12040702	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12568258	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16853894	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2793816	0.84[CHD][hapmap]
rs28523347	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2862617	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4287132	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4652361	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59340306	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6425525	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6425527	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6425529	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6425532	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6679558	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6680823	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6682127	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6682247	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6692684	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6704528	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72713496	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72713497	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72715509	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72715598	0.90[ASN][1000 genomes]
rs7531307	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap];0.91[ASN][1000 genomes]
rs7553899	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9804166	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005278	chr1:179197645-179371395	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10913708	FAM20B	cis	parietal	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179261800-179265800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr1:179262200-179264400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
3	chr1:179262200-179264400	Active TSS	HSMM	muscle
4	chr1:179262200-179264800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
5	chr1:179262400-179264400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
6	chr1:179262400-179264400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr1:179262400-179264400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr1:179262400-179264400	Active TSS	Left Ventricle	heart
9	chr1:179262400-179264400	Active TSS	Ovary	ovary
10	chr1:179262400-179264600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr1:179262400-179264600	Active TSS	Brain Germinal Matrix	brain
12	chr1:179262400-179264600	Active TSS	Pancreas	Pancrea
13	chr1:179262400-179264600	Active TSS	Psoas Muscle	Psoas
14	chr1:179262400-179264800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
15	chr1:179262400-179264800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr1:179262600-179264400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:179262600-179264400	Active TSS	Brain Anterior Caudate	brain
18	chr1:179262600-179264400	Active TSS	Sigmoid Colon	Sigmoid Colon
19	chr1:179262600-179264600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr1:179262800-179264400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:179262800-179264600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr1:179262800-179264800	Active TSS	NHLF	lung
23	chr1:179263400-179264600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr1:179263400-179264800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr1:179263600-179264400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
26	chr1:179263600-179264400	Flanking Active TSS	Primary hematopoietic stem cells	blood
27	chr1:179263600-179264600	Flanking Active TSS	Primary B cells from cord blood	blood
28	chr1:179263600-179264800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
29	chr1:179263600-179264800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
30	chr1:179263600-179264800	Enhancers	Fetal Heart	heart
31	chr1:179263600-179266600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
32	chr1:179263800-179264400	Enhancers	Fetal Thymus	thymus
33	chr1:179263800-179264600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr1:179263800-179264600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
35	chr1:179263800-179264600	Flanking Active TSS	Fetal Intestine Small	intestine
36	chr1:179263800-179264800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr1:179263800-179264800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
38	chr1:179263800-179264800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
39	chr1:179263800-179264800	Enhancers	Placenta Amnion	Placenta Amnion
40	chr1:179263800-179264800	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr1:179263800-179265000	Flanking Active TSS	Dnd41	blood
42	chr1:179263800-179267600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr1:179263800-179268400	Enhancers	Primary B cells from peripheral blood	blood
44	chr1:179263800-179304600	Weak transcription	Lung	lung
45	chr1:179263800-179306400	Weak transcription	Gastric	stomach
46	chr1:179264000-179264400	Flanking Active TSS	Liver	Liver
47	chr1:179264000-179264400	Flanking Active TSS	Brain Cingulate Gyrus	brain
48	chr1:179264000-179264400	Flanking Active TSS	Fetal Lung	lung
49	chr1:179264000-179264400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
50	chr1:179264000-179264400	Flanking Active TSS	Stomach Smooth Muscle	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links