Variant report

Variant	rs1823762
Chromosome Location	chr4:86744000-86744001
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11936781	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12498568	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12506184	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1563000	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17010957	0.85[CEU][hapmap];0.85[GIH][hapmap]
rs17010961	0.85[CEU][hapmap];0.91[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs17011002	0.91[ASN][1000 genomes]
rs17011024	0.92[CHB][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17011039	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57129466	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57343585	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60565316	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61163122	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72976750	0.91[ASN][1000 genomes]
rs72976751	0.91[ASN][1000 genomes]
rs72978881	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	esv3450999	chr4:86485840-86773745	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
2	nsv879518	chr4:86739805-86778943	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1823762	THAP9	cis	parietal	SCAN
rs1823762	SPARCL1	cis	cerebellum	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:86728200-86747200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr4:86729000-86744600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr4:86729400-86747400	Weak transcription	Colon Smooth Muscle	Colon
4	chr4:86729800-86744600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr4:86736200-86748600	Weak transcription	Fetal Muscle Trunk	muscle
6	chr4:86737600-86744600	Weak transcription	K562	blood
7	chr4:86737600-86763200	Weak transcription	Primary B cells from cord blood	blood
8	chr4:86740200-86744600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr4:86740200-86744600	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr4:86740200-86744800	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr4:86740200-86745000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr4:86740200-86747000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr4:86740200-86747200	Weak transcription	Fetal Lung	lung
14	chr4:86740200-86748600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr4:86740200-86748800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr4:86741600-86744200	Weak transcription	HSMM	muscle
17	chr4:86741600-86744600	Weak transcription	Fetal Muscle Leg	muscle
18	chr4:86741600-86745800	Weak transcription	Primary B cells from peripheral blood	blood
19	chr4:86741800-86744200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr4:86741800-86747200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr4:86742400-86744400	Enhancers	HUVEC	blood vessel
22	chr4:86742400-86744600	Enhancers	NHDF-Ad	bronchial
23	chr4:86743000-86744000	Enhancers	Fetal Kidney	kidney
24	chr4:86743000-86746000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr4:86743200-86745800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr4:86743200-86748800	Enhancers	Muscle Satellite Cultured Cells	--
27	chr4:86743400-86744000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr4:86743400-86745800	Enhancers	Osteobl	bone
29	chr4:86743600-86744600	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr4:86743600-86744600	Weak transcription	NHLF	lung
31	chr4:86743600-86744800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr4:86743600-86747200	Enhancers	ES-I3 Cell Line	embryonic stem cell
33	chr4:86743800-86744400	Weak transcription	Stomach Smooth Muscle	stomach
34	chr4:86743800-86744600	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr4:86743800-86744600	Weak transcription	HSMMtube	muscle
36	chr4:86743800-86747200	Weak transcription	Aorta	Aorta
37	chr4:86744000-86744400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr4:86744000-86744400	Weak transcription	Fetal Kidney	kidney

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links