Variant report

Variant	rs10516162
Chromosome Location	chr4:57936920-57936921
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	FOS	chr4:57936650-57936959	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr4:57936579-57937416	HUVEC	blood vessel:	n/a	n/a
3	KAP1	chr4:57936665-57937892	HEK293	kidney:	n/a	n/a
4	FOS	chr4:57936673-57936961	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr4:57936902-57936920	HUVEC	blood vessel:	n/a	n/a

Variant related genes	Relation type
UBE2CP3	TF binding region

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11573051	0.80[CEU][hapmap];0.91[AMR][1000 genomes]
rs11573063	0.81[CEU][hapmap];0.91[AMR][1000 genomes]
rs11573068	0.91[AMR][1000 genomes]
rs11934877	0.80[CEU][hapmap];0.91[AMR][1000 genomes]
rs11938043	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17183073	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs17183228	0.93[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17183249	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17761305	0.93[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17787988	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3806744	0.80[CEU][hapmap];0.83[AMR][1000 genomes]
rs3849657	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3849658	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3986230	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4865174	1.00[CEU][hapmap];0.84[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4865178	0.82[AMR][1000 genomes]
rs58389605	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60727341	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs62308265	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62308280	0.92[AMR][1000 genomes]
rs6829171	0.83[ASN][1000 genomes]

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	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	esv3393902	chr4:57935600-57939401	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57899600-57942200	Weak transcription	Primary hematopoietic stem cells	blood
2	chr4:57923800-57937200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr4:57927000-57937400	Weak transcription	Small Intestine	intestine
4	chr4:57929600-57944400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr4:57930800-57937400	Weak transcription	Fetal Kidney	kidney
6	chr4:57931200-57937000	Weak transcription	Brain Cingulate Gyrus	brain
7	chr4:57931600-57940600	Weak transcription	Hela-S3	cervix
8	chr4:57931800-57938800	Weak transcription	Pancreas	Pancrea
9	chr4:57932400-57945600	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr4:57932400-57947600	Genic enhancers	Osteobl	bone
11	chr4:57932600-57937200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr4:57932600-57937200	Weak transcription	Adipose Nuclei	Adipose
13	chr4:57932600-57937200	Weak transcription	Fetal Intestine Large	intestine
14	chr4:57932600-57937600	Weak transcription	Stomach Smooth Muscle	stomach
15	chr4:57932600-57944000	Weak transcription	Fetal Stomach	stomach
16	chr4:57934400-57951600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr4:57934600-57948200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr4:57935200-57937000	Weak transcription	NHDF-Ad	bronchial
19	chr4:57935200-57937800	Enhancers	Aorta	Aorta
20	chr4:57935400-57937200	Weak transcription	Colon Smooth Muscle	Colon
21	chr4:57935600-57937200	Weak transcription	Ovary	ovary
22	chr4:57935600-57937200	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr4:57935600-57937200	Weak transcription	HSMM	muscle
24	chr4:57935600-57937200	Weak transcription	HSMMtube	muscle
25	chr4:57935600-57944000	Weak transcription	Fetal Thymus	thymus
26	chr4:57935800-57937200	Weak transcription	Fetal Heart	heart
27	chr4:57935800-57937200	Weak transcription	Right Atrium	heart
28	chr4:57935800-57937400	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr4:57935800-57937800	Weak transcription	Lung	lung
30	chr4:57935800-57938800	Weak transcription	Right Ventricle	heart
31	chr4:57935800-57940000	Weak transcription	Spleen	Spleen
32	chr4:57935800-57941000	Weak transcription	HUVEC	blood vessel
33	chr4:57935800-57945000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr4:57935800-57948000	Weak transcription	Fetal Muscle Leg	muscle
35	chr4:57936000-57937000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr4:57936000-57937400	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr4:57936000-57938000	Enhancers	HMEC	breast
38	chr4:57936200-57937000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr4:57936200-57937200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr4:57936200-57937200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr4:57936200-57937200	Weak transcription	Left Ventricle	heart
42	chr4:57936200-57938000	Enhancers	Primary monocytes fromperipheralblood	blood
43	chr4:57936200-57938000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr4:57936200-57938800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr4:57936200-57945000	Weak transcription	Fetal Muscle Trunk	muscle
46	chr4:57936400-57937000	Strong transcription	NH-A	brain
47	chr4:57936400-57938000	Enhancers	NHEK	skin
48	chr4:57936400-57939200	Enhancers	A549	lung
49	chr4:57936400-57942000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr4:57936600-57937800	Enhancers	Pancreatic Islets	Pancreatic Islet

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links