Variant report

Variant	rs4876679
Chromosome Location	chr8:117763873-117763874
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:117763503..117766300-chr8:117766342..117768471,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000147677	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10088177	0.84[AFR][1000 genomes]
rs10094452	0.87[CHB][hapmap];0.92[JPT][hapmap];0.92[ASN][1000 genomes]
rs10095889	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10104144	0.82[ASN][1000 genomes]
rs10112604	0.84[AFR][1000 genomes]
rs10283122	0.81[CHD][hapmap];0.85[ASN][1000 genomes]
rs10283129	0.93[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10808485	0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs12548402	0.83[ASN][1000 genomes]
rs12675074	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12675093	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1317271	0.93[YRI][hapmap]
rs13258789	0.92[ASN][1000 genomes]
rs13266314	0.81[CHB][hapmap];0.92[CHD][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs1436767	0.81[CHD][hapmap];0.92[JPT][hapmap]
rs1529945	0.93[YRI][hapmap]
rs17664079	0.81[CHD][hapmap];0.92[JPT][hapmap]
rs2121339	0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs34672734	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34701891	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35682273	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4145242	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4372028	0.81[CHD][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs4449824	0.87[CHB][hapmap];0.92[CHD][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs4464999	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4514005	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4876675	0.92[ASN][1000 genomes]
rs4876680	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55951040	0.82[AFR][1000 genomes]
rs62510194	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6469660	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6983034	0.90[ASN][1000 genomes]
rs6990665	0.92[JPT][hapmap]
rs6992589	0.81[CHD][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs7014156	0.92[JPT][hapmap]
rs7814084	0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs7820778	0.93[YRI][hapmap]
rs7823870	0.84[ASN][1000 genomes]
rs7831811	0.81[YRI][hapmap]
rs7833618	0.81[YRI][hapmap]
rs7836226	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7836549	0.93[YRI][hapmap]
rs7843792	0.81[CHD][hapmap];0.92[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530386	chr8:117509968-118391406	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	esv3430552	chr8:117762521-117764519	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4876679	EXT1	cis	cerebellum	SCAN
rs4876679	NOV	cis	cerebellum	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:117733600-117766600	Weak transcription	Fetal Lung	lung
2	chr8:117733600-117766800	Weak transcription	Adipose Nuclei	Adipose
3	chr8:117734400-117766800	Weak transcription	Fetal Stomach	stomach
4	chr8:117734600-117766200	Weak transcription	Fetal Muscle Leg	muscle
5	chr8:117734600-117766400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr8:117734600-117766800	Weak transcription	Fetal Intestine Small	intestine
7	chr8:117734600-117767200	Weak transcription	Fetal Muscle Trunk	muscle
8	chr8:117734800-117766200	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr8:117735000-117766000	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr8:117735000-117766200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr8:117737400-117766600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr8:117737600-117766800	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr8:117737800-117767200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr8:117738200-117766400	Weak transcription	Placenta	Placenta
15	chr8:117738400-117764200	Weak transcription	Primary hematopoietic stem cells	blood
16	chr8:117739000-117766000	Weak transcription	Liver	Liver
17	chr8:117741000-117766800	Weak transcription	Duodenum Mucosa	Duodenum
18	chr8:117741200-117764400	Weak transcription	HepG2	liver
19	chr8:117741200-117767400	Weak transcription	Aorta	Aorta
20	chr8:117742800-117766400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr8:117742800-117767400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr8:117744000-117766800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr8:117744200-117766400	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr8:117744400-117766200	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr8:117745600-117766600	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr8:117745600-117766800	Weak transcription	Right Ventricle	heart
27	chr8:117745800-117765800	Weak transcription	Brain Hippocampus Middle	brain
28	chr8:117748000-117764000	Weak transcription	HMEC	breast
29	chr8:117748200-117767000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr8:117748200-117767400	Weak transcription	Lung	lung
31	chr8:117748400-117766800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr8:117748800-117765800	Weak transcription	HUVEC	blood vessel
33	chr8:117748800-117766800	Weak transcription	Psoas Muscle	Psoas
34	chr8:117749000-117766800	Weak transcription	Fetal Intestine Large	intestine
35	chr8:117752600-117765600	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr8:117752600-117766600	Weak transcription	Brain Cingulate Gyrus	brain
37	chr8:117752800-117766400	Weak transcription	Small Intestine	intestine
38	chr8:117752800-117766800	Weak transcription	Brain Substantia Nigra	brain
39	chr8:117752800-117766800	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr8:117753000-117766000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr8:117753200-117765800	Weak transcription	NHLF	lung
42	chr8:117753200-117766200	Weak transcription	Stomach Smooth Muscle	stomach
43	chr8:117753200-117766600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr8:117753200-117766800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr8:117753200-117766800	Weak transcription	Brain Germinal Matrix	brain
46	chr8:117753200-117766800	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr8:117753200-117766800	Weak transcription	HSMM	muscle
48	chr8:117753200-117766800	Weak transcription	NHDF-Ad	bronchial
49	chr8:117753200-117767200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr8:117754000-117766200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links