Variant report

Variant	rs11189312
Chromosome Location	chr10:99424242-99424243
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	chr10:99412413..99414707-chr10:99422653..99425791,3	K562	blood:
2	chr10:99423436..99426150-chr10:99432086..99434715,3	K562	blood:

Extended variants
information (count: 18 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs10882983	0.96[EUR][1000 genomes]
rs10882987	1.00[CEU][hapmap];0.88[GIH][hapmap];0.96[TSI][hapmap];0.85[YRI][hapmap];0.91[EUR][1000 genomes]
rs10882990	0.84[CEU][hapmap]
rs11189321	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.94[LWK][hapmap];0.92[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11189324	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11189328	1.00[CEU][hapmap]
rs12049715	0.91[EUR][1000 genomes]
rs12219065	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2065671	0.96[EUR][1000 genomes]
rs2065672	1.00[CEU][hapmap];0.95[GIH][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.96[EUR][1000 genomes]
rs3818780	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4291605	0.95[EUR][1000 genomes]
rs45491602	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4561136	0.87[CHB][hapmap]
rs57574145	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7072085	1.00[CEU][hapmap];0.91[EUR][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	esv1817777	chr10:99196035-99558169	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv1045292	chr10:99411153-99450861	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11189312	FRAT2	cis	cerebellum	SCAN
rs11189312	PI4K2A	cis	parietal	SCAN
rs11189312	ZNF518A	cis	cerebellum	SCAN
rs11189312	AVPI1	cis	parietal	SCAN
rs11189312	FRAT1	cis	cerebellum	SCAN
rs11189312	C10orf62	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:99401800-99443600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr10:99402000-99444600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr10:99408600-99433400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr10:99409200-99444800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr10:99409400-99445800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr10:99410200-99431800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr10:99410400-99436200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr10:99410400-99436200	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr10:99410600-99431200	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr10:99411000-99437000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr10:99411600-99433400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr10:99411600-99437800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr10:99412800-99429000	Weak transcription	Primary hematopoietic stem cells	blood
14	chr10:99413000-99433400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr10:99413200-99433600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr10:99416400-99426000	Weak transcription	Hela-S3	cervix
17	chr10:99416800-99425800	Weak transcription	Right Ventricle	heart
18	chr10:99416800-99426000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr10:99416800-99426600	Weak transcription	Small Intestine	intestine
20	chr10:99416800-99428800	Weak transcription	Psoas Muscle	Psoas
21	chr10:99417000-99424600	Weak transcription	Colonic Mucosa	Colon
22	chr10:99417000-99425800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr10:99417000-99425800	Weak transcription	Gastric	stomach
24	chr10:99417000-99425800	Weak transcription	Ovary	ovary
25	chr10:99417200-99425800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr10:99418000-99425800	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr10:99418400-99425800	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr10:99418600-99425800	Weak transcription	GM12878-XiMat	blood
29	chr10:99419000-99425800	Weak transcription	HUVEC	blood vessel
30	chr10:99419400-99433600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr10:99420400-99429400	Strong transcription	HMEC	breast
32	chr10:99420600-99429000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr10:99420600-99431800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr10:99420800-99436200	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr10:99421000-99427600	Strong transcription	Muscle Satellite Cultured Cells	--
36	chr10:99421000-99428400	Strong transcription	NHDF-Ad	bronchial
37	chr10:99421000-99431800	Strong transcription	Cortex derived primary cultured neurospheres	brain
38	chr10:99421000-99433600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr10:99421200-99430600	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr10:99421200-99431000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr10:99421200-99431200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr10:99421200-99431600	Strong transcription	NHEK	skin
43	chr10:99421200-99433600	Strong transcription	Osteobl	bone
44	chr10:99421200-99433800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr10:99421200-99436200	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chr10:99421400-99425000	Strong transcription	Primary T cells from cord blood	blood
47	chr10:99421400-99429600	Strong transcription	Brain Hippocampus Middle	brain
48	chr10:99421400-99429800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr10:99421400-99430400	Strong transcription	Primary T helper cells fromperipheralblood	blood
50	chr10:99421400-99430600	Genic enhancers	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links