Variant report

Variant	rs10809920
Chromosome Location	chr9:13237530-13237531
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:13236159..13239673-chr9:13240021..13241602,3	K562	blood:

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10116304	0.86[JPT][hapmap]
rs10116749	0.86[JPT][hapmap]
rs10122431	0.86[JPT][hapmap]
rs10125770	0.81[JPT][hapmap]
rs1038979	1.00[YRI][hapmap]
rs10511577	0.86[JPT][hapmap]
rs10738323	0.81[JPT][hapmap]
rs10738324	0.86[JPT][hapmap]
rs10738325	0.81[JPT][hapmap]
rs10756454	0.86[JPT][hapmap]
rs10756455	0.86[JPT][hapmap]
rs10756456	0.86[JPT][hapmap]
rs10756457	0.82[JPT][hapmap]
rs10756461	0.83[LWK][hapmap];1.00[YRI][hapmap]
rs10809907	0.86[JPT][hapmap]
rs10809912	0.86[JPT][hapmap]
rs10960955	0.86[JPT][hapmap]
rs12351444	0.86[JPT][hapmap]
rs1330129	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.95[EUR][1000 genomes]
rs1331668	0.86[JPT][hapmap]
rs1331670	0.81[JPT][hapmap]
rs1331672	0.86[JPT][hapmap]
rs1331673	0.86[JPT][hapmap]
rs1331674	0.86[JPT][hapmap]
rs1331675	0.86[JPT][hapmap]
rs1360058	0.81[JPT][hapmap]
rs1556421	0.86[JPT][hapmap]
rs16930137	0.81[JPT][hapmap]
rs17273898	0.87[ASW][hapmap];0.89[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1854907	0.86[JPT][hapmap]
rs1854908	0.86[JPT][hapmap]
rs1854909	0.86[JPT][hapmap]
rs1929541	0.86[JPT][hapmap]
rs1999393	0.86[JPT][hapmap]
rs2274856	0.86[JPT][hapmap]
rs2297003	0.81[JPT][hapmap]
rs3818595	0.81[JPT][hapmap]
rs6474753	0.86[JPT][hapmap]
rs6474754	0.86[JPT][hapmap]
rs7024892	0.86[JPT][hapmap]
rs7035244	0.86[JPT][hapmap]
rs7037618	0.86[JPT][hapmap]
rs7040347	0.86[JPT][hapmap]
rs7043857	0.96[ASN][1000 genomes]
rs72706378	0.95[EUR][1000 genomes]
rs7859465	0.86[JPT][hapmap]
rs7867993	0.81[JPT][hapmap]
rs7871575	0.86[JPT][hapmap]
rs9886797	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv892578	chr9:12942956-13485035	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv892583	chr9:13166139-13350478	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv892584	chr9:13214871-13350478	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv427838	chr9:13229753-13393890	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10809920	ZDHHC21	cis	parietal	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:13164200-13248600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr9:13164200-13258800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr9:13189000-13268600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr9:13190400-13237800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr9:13202800-13250600	Weak transcription	Pancreas	Pancrea
6	chr9:13202800-13250800	Weak transcription	Psoas Muscle	Psoas
7	chr9:13203000-13261000	Weak transcription	Colon Smooth Muscle	Colon
8	chr9:13203400-13247000	Weak transcription	Brain Cingulate Gyrus	brain
9	chr9:13203600-13245600	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr9:13204000-13241800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr9:13204000-13249200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr9:13204200-13244600	Weak transcription	HepG2	liver
13	chr9:13206000-13247000	Weak transcription	Brain Angular Gyrus	brain
14	chr9:13208200-13265000	Weak transcription	Aorta	Aorta
15	chr9:13209800-13266000	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr9:13216600-13247000	Weak transcription	Fetal Brain Female	brain
17	chr9:13217000-13244200	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr9:13219800-13265600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr9:13221600-13241600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr9:13221600-13244200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr9:13221600-13245400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr9:13221800-13242800	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr9:13221800-13246600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr9:13222600-13238000	Weak transcription	Adipose Nuclei	Adipose
25	chr9:13222600-13246200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr9:13223800-13239600	Weak transcription	HSMM	muscle
27	chr9:13224000-13241400	Weak transcription	Ovary	ovary
28	chr9:13224000-13242200	Weak transcription	Fetal Stomach	stomach
29	chr9:13224000-13264600	Weak transcription	Osteobl	bone
30	chr9:13224200-13241800	Weak transcription	Fetal Muscle Leg	muscle
31	chr9:13224200-13245600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr9:13224400-13242600	Weak transcription	Fetal Lung	lung
33	chr9:13224400-13252400	Weak transcription	Liver	Liver
34	chr9:13224600-13241800	Weak transcription	Fetal Muscle Trunk	muscle
35	chr9:13224600-13242400	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr9:13224600-13247000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr9:13226000-13252800	Weak transcription	Fetal Heart	heart
38	chr9:13226400-13247000	Weak transcription	Stomach Smooth Muscle	stomach
39	chr9:13226600-13242600	Weak transcription	Left Ventricle	heart
40	chr9:13226600-13259200	Weak transcription	Right Ventricle	heart
41	chr9:13226800-13278000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr9:13229400-13247200	Weak transcription	HSMMtube	muscle
43	chr9:13230200-13242400	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr9:13230600-13241400	Weak transcription	HUVEC	blood vessel
45	chr9:13232400-13264800	Weak transcription	NH-A	brain
46	chr9:13233800-13255400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr9:13235600-13244000	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr9:13235800-13247200	Weak transcription	Brain Germinal Matrix	brain
49	chr9:13236400-13238800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr9:13236400-13248000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links