Variant report

Variant	rs10025599
Chromosome Location	chr4:79791119-79791120
allele	C/T
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	POLR2A	chr4:79789328-79795194	K562	blood:	n/a	n/a

Variant related genes	Relation type
BMP2K	TF binding region

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10018189	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10023100	0.89[ASN][1000 genomes]
rs10034295	0.86[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs11724233	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs1275045	0.92[ASN][1000 genomes]
rs1275046	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1275047	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs13108247	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs13138117	0.95[CEU][hapmap]
rs1480718	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1979444	1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs2046104	0.81[ASN][1000 genomes]
rs2288254	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2554395	0.82[ASN][1000 genomes]
rs3822106	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3937772	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4246708	0.81[ASN][1000 genomes]
rs4472162	0.80[JPT][hapmap]
rs4512020	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs62308043	0.87[ASN][1000 genomes]
rs6533951	0.80[CHB][hapmap];0.85[JPT][hapmap]
rs6534083	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6534085	0.98[ASN][1000 genomes]
rs6534086	0.98[ASN][1000 genomes]
rs6534087	0.98[ASN][1000 genomes]
rs6534090	0.80[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs6846743	0.85[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs6854347	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7656083	0.98[ASN][1000 genomes]
rs7688534	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[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	nsv879504	chr4:79759796-79874275	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79738800-79793200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr4:79744600-79793800	Weak transcription	Psoas Muscle	Psoas
3	chr4:79747200-79815600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr4:79748800-79823600	Weak transcription	Small Intestine	intestine
5	chr4:79749200-79793600	Weak transcription	Brain Cingulate Gyrus	brain
6	chr4:79749400-79792400	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr4:79749400-79793800	Weak transcription	Gastric	stomach
8	chr4:79749600-79793000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr4:79749600-79793600	Weak transcription	Brain Germinal Matrix	brain
10	chr4:79749600-79793800	Weak transcription	Fetal Brain Female	brain
11	chr4:79749800-79793400	Weak transcription	Thymus	Thymus
12	chr4:79749800-79793600	Weak transcription	Colonic Mucosa	Colon
13	chr4:79750400-79791400	Weak transcription	Colon Smooth Muscle	Colon
14	chr4:79750400-79792200	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr4:79750400-79792600	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr4:79750400-79793600	Weak transcription	Stomach Smooth Muscle	stomach
17	chr4:79750400-79797000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr4:79750600-79792600	Weak transcription	HSMMtube	muscle
19	chr4:79750600-79793600	Weak transcription	Fetal Kidney	kidney
20	chr4:79759600-79792400	Weak transcription	Rectal Smooth Muscle	rectum
21	chr4:79760000-79792400	Weak transcription	Fetal Lung	lung
22	chr4:79760600-79794800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr4:79761000-79791800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr4:79764600-79792400	Weak transcription	Brain Anterior Caudate	brain
25	chr4:79768400-79811400	Weak transcription	Hela-S3	cervix
26	chr4:79771400-79801000	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr4:79772800-79792000	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr4:79774400-79793600	Weak transcription	Right Ventricle	heart
29	chr4:79774600-79793400	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr4:79774800-79793200	Weak transcription	Brain Hippocampus Middle	brain
31	chr4:79776000-79792000	Weak transcription	Esophagus	oesophagus
32	chr4:79777200-79792400	Weak transcription	Brain Angular Gyrus	brain
33	chr4:79779000-79792400	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr4:79779000-79814400	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr4:79779600-79791800	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr4:79779800-79858200	Weak transcription	Fetal Brain Male	brain
37	chr4:79781400-79793000	Weak transcription	Ovary	ovary
38	chr4:79782000-79793800	Weak transcription	Aorta	Aorta
39	chr4:79782400-79792200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr4:79782800-79792400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr4:79783200-79801000	Strong transcription	K562	blood
42	chr4:79784000-79793800	Weak transcription	A549	lung
43	chr4:79784000-79811200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr4:79785000-79793000	Weak transcription	HepG2	liver
45	chr4:79785000-79793800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr4:79785000-79832400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr4:79785200-79793800	Weak transcription	NHEK	skin
48	chr4:79785400-79793600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr4:79785600-79792000	Weak transcription	Pancreas	Pancrea
50	chr4:79785600-79793600	Weak transcription	GM12878-XiMat	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links