Variant report

Variant	rs17050208
Chromosome Location	chr4:119890865-119890866
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:119890629..119893657-chr4:119893845..119896663,3	K562	blood:
2	chr4:119693011..119693928-chr4:119890256..119890896,2	MCF-7	breast:
3	chr4:119661926..119662579-chr4:119890197..119891151,3	MCF-7	breast:
4	chr4:119692998..119693937-chr4:119890592..119891412,2	K562	blood:

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10017229	0.84[JPT][hapmap]
rs10434026	0.82[ASN][1000 genomes]
rs10518316	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13108576	0.82[ASN][1000 genomes]
rs13111284	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13117365	0.83[ASN][1000 genomes]
rs17050193	0.81[ASN][1000 genomes]
rs17050228	0.84[JPT][hapmap]
rs17327171	0.83[LWK][hapmap]
rs28667954	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs36116256	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9307465	0.84[MEX][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	nsv916641	chr4:119780023-120777320	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv948802	chr4:119844269-120208926	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17050208	PRSS12	cis	parietal	SCAN
rs17050208	NDST3	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:119879800-119893400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr4:119886600-119896800	Enhancers	Rectal Smooth Muscle	rectum
3	chr4:119889400-119894400	Weak transcription	Esophagus	oesophagus
4	chr4:119889600-119893000	Weak transcription	Primary B cells from cord blood	blood
5	chr4:119889800-119896200	Weak transcription	Fetal Thymus	thymus
6	chr4:119890000-119891200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr4:119890000-119892800	Weak transcription	Psoas Muscle	Psoas
8	chr4:119890000-119892800	Weak transcription	Right Atrium	heart
9	chr4:119890000-119895400	Weak transcription	Left Ventricle	heart
10	chr4:119890400-119891000	Active TSS	Aorta	Aorta
11	chr4:119890400-119891000	Enhancers	HSMM	muscle
12	chr4:119890400-119892600	Weak transcription	Ovary	ovary
13	chr4:119890400-119892800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr4:119890400-119893400	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr4:119890400-119894800	Weak transcription	NHLF	lung
16	chr4:119890400-119895800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr4:119890400-119895800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr4:119890400-119896000	Weak transcription	Right Ventricle	heart
19	chr4:119890400-119896000	Weak transcription	NH-A	brain
20	chr4:119890400-119896400	Enhancers	Colon Smooth Muscle	Colon
21	chr4:119890600-119891000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr4:119890600-119891000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr4:119890600-119891000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr4:119890600-119892000	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr4:119890600-119892400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr4:119890600-119892600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr4:119890600-119892800	Enhancers	Stomach Smooth Muscle	stomach
28	chr4:119890600-119893600	Weak transcription	Osteobl	bone
29	chr4:119890600-119894400	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr4:119890600-119895400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr4:119890600-119895600	Weak transcription	HMEC	breast
32	chr4:119890600-119896000	Weak transcription	Adipose Nuclei	Adipose
33	chr4:119890600-119898200	Weak transcription	Fetal Stomach	stomach
34	chr4:119890800-119892600	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr4:119890800-119892800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr4:119890800-119893000	Weak transcription	Fetal Kidney	kidney
37	chr4:119890800-119893600	Weak transcription	Fetal Heart	heart
38	chr4:119890800-119894600	Weak transcription	NHDF-Ad	bronchial
39	chr4:119890800-119895400	Weak transcription	Fetal Intestine Large	intestine
40	chr4:119890800-119895400	Weak transcription	Small Intestine	intestine
41	chr4:119890800-119895600	Weak transcription	Fetal Intestine Small	intestine
42	chr4:119890800-119896200	Weak transcription	Duodenum Mucosa	Duodenum
43	chr4:119890800-119896200	Weak transcription	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links