Variant report

Variant	rs10820954
Chromosome Location	chr9:94970458-94970459
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	chr9:94894716..94897374-chr9:94969241..94971639,2	K562	blood:
2	chr9:94946211..94948106-chr9:94969789..94972073,2	K562	blood:

Extended variants
information (count: 40 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10081693	1.00[ASN][1000 genomes]
rs10119535	0.94[CEU][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10123080	0.91[ASN][1000 genomes]
rs10156530	0.91[ASN][1000 genomes]
rs10283718	1.00[ASN][1000 genomes]
rs10820949	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10820956	0.95[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10820962	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10820963	0.94[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10820970	1.00[ASN][1000 genomes]
rs10820973	1.00[ASN][1000 genomes]
rs10992265	0.91[ASN][1000 genomes]
rs10992266	1.00[ASN][1000 genomes]
rs10992267	1.00[ASN][1000 genomes]
rs10992270	1.00[ASN][1000 genomes]
rs10992308	0.89[CEU][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];1.00[ASN][1000 genomes]
rs10992312	0.89[CEU][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];1.00[ASN][1000 genomes]
rs10992314	1.00[ASN][1000 genomes]
rs10992334	1.00[ASN][1000 genomes]
rs12345822	1.00[ASN][1000 genomes]
rs12349712	1.00[ASN][1000 genomes]
rs12352447	1.00[ASN][1000 genomes]
rs1447114	0.94[CEU][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1951849	1.00[ASN][1000 genomes]
rs3889951	1.00[ASN][1000 genomes]
rs58391046	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60993552	1.00[ASN][1000 genomes]
rs6479412	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6479413	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7036078	0.90[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7860297	1.00[ASN][1000 genomes]
rs7863859	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7872739	1.00[ASN][1000 genomes]
rs7873882	0.95[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9695754	0.95[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949008	chr9:94500776-95182133	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1050845	chr9:94687959-95312406	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv1046733	chr9:94690622-95138564	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv530947	chr9:94697309-95093377	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv917089	chr9:94857047-95099848	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10820954	CENPP	cis	Esophagus Muscularis	GTEx
rs10820954	NOL8	Cis_1M	lymphoblastoid	RTeQTL
rs10820954	CENPP	cis	Artery Tibial	GTEx
rs10820954	CENPP	cis	Nerve Tibial	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94954400-94971000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr9:94959400-94971200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr9:94959400-94973200	Weak transcription	Pancreas	Pancrea
4	chr9:94959600-94970800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr9:94966000-94973400	Weak transcription	Esophagus	oesophagus
6	chr9:94966600-94971200	Weak transcription	Fetal Intestine Large	intestine
7	chr9:94966800-94970800	Weak transcription	Adipose Nuclei	Adipose
8	chr9:94967000-94971000	Weak transcription	HSMM	muscle
9	chr9:94967200-94970800	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr9:94967200-94970800	Weak transcription	HSMMtube	muscle
11	chr9:94967400-94971000	Weak transcription	Brain Anterior Caudate	brain
12	chr9:94967400-94971000	Weak transcription	Fetal Brain Female	brain
13	chr9:94967600-94971000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr9:94967600-94971000	Weak transcription	Primary hematopoietic stem cells	blood
15	chr9:94967600-94971400	Weak transcription	Rectal Smooth Muscle	rectum
16	chr9:94967800-94970800	Weak transcription	Brain Hippocampus Middle	brain
17	chr9:94967800-94970800	Weak transcription	Psoas Muscle	Psoas
18	chr9:94967800-94971200	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr9:94968000-94970800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr9:94968000-94970800	Weak transcription	Fetal Muscle Trunk	muscle
21	chr9:94968200-94970600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr9:94968200-94970600	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr9:94968200-94970600	Weak transcription	HMEC	breast
24	chr9:94968200-94970800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr9:94968200-94971000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr9:94968200-94971000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr9:94968200-94971000	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr9:94968400-94971000	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr9:94968600-94970800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr9:94968600-94971200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr9:94968800-94970800	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr9:94968800-94971000	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr9:94968800-94971200	Weak transcription	Fetal Stomach	stomach
34	chr9:94968800-94971400	Weak transcription	Right Ventricle	heart
35	chr9:94968800-94972000	Weak transcription	Fetal Intestine Small	intestine
36	chr9:94968800-94976800	Strong transcription	A549	lung
37	chr9:94969000-94970600	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr9:94969000-94970600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr9:94969000-94970600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr9:94969000-94970800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr9:94969000-94970800	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr9:94969000-94970800	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr9:94969000-94970800	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr9:94969000-94970800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr9:94969000-94970800	Weak transcription	Placenta	Placenta
46	chr9:94969000-94970800	Weak transcription	Dnd41	blood
47	chr9:94969000-94970800	Weak transcription	NHDF-Ad	bronchial
48	chr9:94969000-94970800	Weak transcription	NHLF	lung
49	chr9:94969000-94971000	Weak transcription	HepG2	liver
50	chr9:94969000-94971000	Weak transcription	HUVEC	blood vessel

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