Variant report

Variant	rs17134002
Chromosome Location	chr7:50808087-50808088
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	chr7:50804663..50812652-chr7:50812790..50817860,10	K562	blood:

Variant related genes	Relation type
ENSG00000106070	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1019000	0.84[CEU][hapmap];0.87[TSI][hapmap]
rs1019002	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs1024529	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10273302	0.80[CEU][hapmap]
rs10278363	0.83[CEU][hapmap];0.89[JPT][hapmap]
rs11238339	0.81[CEU][hapmap]
rs12536500	0.88[CEU][hapmap];0.80[CHB][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12665949	0.80[CEU][hapmap];0.81[JPT][hapmap]
rs13236710	0.90[CHB][hapmap];0.97[CHD][hapmap]
rs17152120	0.90[CHB][hapmap];0.97[CHD][hapmap]
rs1962390	0.93[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1962391	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1978208	0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs2329424	0.94[CEU][hapmap];0.80[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2329490	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2329491	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2329494	0.92[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2529399	0.90[ASN][1000 genomes]
rs2715119	0.80[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs3779072	0.80[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs4947444	0.88[YRI][hapmap]
rs4947828	0.85[AFR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4947861	0.83[CEU][hapmap];0.83[CHD][hapmap];0.89[JPT][hapmap]
rs6593145	0.86[ASN][1000 genomes]
rs6593182	0.89[JPT][hapmap]
rs6968827	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7383871	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7780348	0.88[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7782797	0.94[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7794299	0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs990358	0.88[YRI][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	nsv1016665	chr7:50452552-51404524	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1031138	chr7:50651793-50814881	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17134002	LOC100129427	cis	parietal	SCAN
rs17134002	VWC2	cis	cerebellum	SCAN
rs17134002	FIGNL1	cis	cerebellum	SCAN
rs17134002	C7orf72	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:50788000-50816000	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr7:50789400-50811600	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr7:50798000-50812000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr7:50798600-50822600	Weak transcription	Ovary	ovary
5	chr7:50798800-50810000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr7:50798800-50811400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr7:50798800-50815200	Weak transcription	Aorta	Aorta
8	chr7:50798800-50815200	Weak transcription	Stomach Smooth Muscle	stomach
9	chr7:50798800-50824800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr7:50798800-50832400	Weak transcription	HSMM	muscle
11	chr7:50798800-50837200	Weak transcription	HSMMtube	muscle
12	chr7:50799000-50815200	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr7:50799000-50817400	Weak transcription	Rectal Smooth Muscle	rectum
14	chr7:50799000-50823000	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr7:50799200-50811400	Weak transcription	Fetal Brain Female	brain
16	chr7:50800400-50811200	Weak transcription	Fetal Stomach	stomach
17	chr7:50801600-50811400	Weak transcription	Osteobl	bone
18	chr7:50801600-50814400	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr7:50802000-50810600	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr7:50802000-50811200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr7:50802000-50814200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr7:50802200-50810000	Weak transcription	Fetal Intestine Large	intestine
23	chr7:50802200-50811200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr7:50802200-50815600	Weak transcription	Placenta	Placenta
25	chr7:50802600-50813200	Weak transcription	Hela-S3	cervix
26	chr7:50802600-50824000	Weak transcription	NH-A	brain
27	chr7:50802800-50814400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr7:50804600-50811600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr7:50806000-50808200	Enhancers	Pancreas	Pancrea
30	chr7:50806400-50811800	Weak transcription	K562	blood
31	chr7:50807000-50808600	Enhancers	HUVEC	blood vessel
32	chr7:50807000-50809200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr7:50807200-50808200	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr7:50807200-50808200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr7:50807200-50808200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr7:50807200-50808200	Enhancers	Brain Angular Gyrus	brain
37	chr7:50807200-50808200	Enhancers	Brain Anterior Caudate	brain
38	chr7:50807200-50808200	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr7:50807200-50808200	Enhancers	Left Ventricle	heart
40	chr7:50807200-50808200	Enhancers	A549	lung
41	chr7:50807200-50809200	Enhancers	Primary hematopoietic stem cells	blood
42	chr7:50807200-50809200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr7:50807400-50808200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr7:50807400-50808200	Enhancers	Primary B cells from cord blood	blood
45	chr7:50807400-50808200	Enhancers	Primary B cells from peripheral blood	blood
46	chr7:50807400-50808200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
47	chr7:50807400-50808200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
48	chr7:50807400-50808200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
49	chr7:50807400-50808200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
50	chr7:50807400-50808200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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