Variant report

Variant	rs2155339
Chromosome Location	chr11:105962546-105962547
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GRIA4-2	chr11:105962194-105965381	NONHSAT023973

Extended variants
information (count: 92 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs1002629	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10047500	0.82[ASN][1000 genomes]
rs10502066	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10502067	0.82[ASN][1000 genomes]
rs10895934	0.82[ASN][1000 genomes]
rs10895937	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11226959	0.82[ASN][1000 genomes]
rs11226961	0.82[ASN][1000 genomes]
rs11226970	0.82[ASN][1000 genomes]
rs11226971	0.82[ASN][1000 genomes]
rs11226972	0.82[ASN][1000 genomes]
rs11226973	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11226974	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11226975	1.00[JPT][hapmap]
rs11226976	0.82[ASN][1000 genomes]
rs11226977	0.82[ASN][1000 genomes]
rs11226978	0.82[ASN][1000 genomes]
rs11226979	0.82[ASN][1000 genomes]
rs11226981	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11226990	0.82[ASN][1000 genomes]
rs1154607	0.82[ASN][1000 genomes]
rs11819920	0.82[ASN][1000 genomes]
rs11819968	0.82[ASN][1000 genomes]
rs11821428	0.82[ASN][1000 genomes]
rs11821642	0.82[ASN][1000 genomes]
rs11823365	1.00[ASN][1000 genomes]
rs11823838	0.82[ASN][1000 genomes]
rs11823993	0.82[ASN][1000 genomes]
rs11824559	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11824707	0.82[ASN][1000 genomes]
rs11824969	1.00[JPT][hapmap];0.82[YRI][hapmap];1.00[ASN][1000 genomes]
rs11825111	0.82[ASN][1000 genomes]
rs11825978	0.82[ASN][1000 genomes]
rs11826475	0.82[ASN][1000 genomes]
rs11826477	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11826484	0.82[ASN][1000 genomes]
rs11826487	0.82[ASN][1000 genomes]
rs11826794	0.82[ASN][1000 genomes]
rs11826859	1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11827132	0.82[ASN][1000 genomes]
rs11827762	0.82[ASN][1000 genomes]
rs11828217	0.82[ASN][1000 genomes]
rs11828435	0.82[ASN][1000 genomes]
rs12271058	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12271522	1.00[ASN][1000 genomes]
rs12276276	0.82[ASN][1000 genomes]
rs12277443	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12277629	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12278043	0.82[ASN][1000 genomes]
rs12283457	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12283643	0.82[ASN][1000 genomes]
rs12283939	0.82[ASN][1000 genomes]
rs12284680	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12286785	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12288968	0.82[ASN][1000 genomes]
rs12289014	0.82[ASN][1000 genomes]
rs12289033	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12289035	0.82[ASN][1000 genomes]
rs12291850	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12294993	0.82[ASN][1000 genomes]
rs17485615	1.00[ASN][1000 genomes]
rs1939809	0.88[EUR][1000 genomes]
rs2186879	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3889602	1.00[CEU][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs55865873	1.00[ASN][1000 genomes]
rs56025631	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56033334	0.82[ASN][1000 genomes]
rs56115097	0.82[ASN][1000 genomes]
rs56167003	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56412913	1.00[ASN][1000 genomes]
rs61361634	0.82[ASN][1000 genomes]
rs61398602	1.00[ASN][1000 genomes]
rs7102241	0.82[ASN][1000 genomes]
rs7106458	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7106459	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7106786	1.00[JPT][hapmap];0.88[YRI][hapmap];1.00[ASN][1000 genomes]
rs7106919	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7109903	0.82[ASN][1000 genomes]
rs7111720	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7115990	0.82[ASN][1000 genomes]
rs7119670	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7120289	0.82[ASN][1000 genomes]
rs7120421	0.82[ASN][1000 genomes]
rs7120578	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7121763	0.82[ASN][1000 genomes]
rs7126319	0.82[ASN][1000 genomes]
rs7126900	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs73537610	0.82[ASN][1000 genomes]
rs73537615	0.82[ASN][1000 genomes]
rs7926902	1.00[ASN][1000 genomes]
rs7935812	1.00[JPT][hapmap];0.88[YRI][hapmap];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048381	chr11:105945117-106561574	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2155339	AASDHPPT	cis	lymphoblastoid	seeQTL
rs2155339	AASDHPPT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:105949000-105973400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr11:105949200-105966000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr11:105949200-105967800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr11:105949200-105969800	Weak transcription	Lung	lung
5	chr11:105949200-105971600	Weak transcription	Esophagus	oesophagus
6	chr11:105950400-105971200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr11:105950600-105969400	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr11:105952000-105969400	Weak transcription	Colonic Mucosa	Colon
9	chr11:105953400-105965600	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr11:105953400-105970600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr11:105953600-105969600	Weak transcription	Gastric	stomach
12	chr11:105954000-105963000	Weak transcription	NHDF-Ad	bronchial
13	chr11:105956000-105970000	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr11:105957200-105971000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr11:105957200-105976600	Weak transcription	Pancreas	Pancrea
16	chr11:105957200-105976800	Weak transcription	Aorta	Aorta
17	chr11:105957800-105968200	Weak transcription	Psoas Muscle	Psoas
18	chr11:105958600-105965200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr11:105958600-105970000	Weak transcription	Fetal Intestine Small	intestine
20	chr11:105958600-105971800	Weak transcription	Hela-S3	cervix
21	chr11:105958800-105962600	Weak transcription	Stomach Smooth Muscle	stomach
22	chr11:105959000-105969000	Weak transcription	Stomach Mucosa	stomach
23	chr11:105959200-105965000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr11:105959200-105970000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr11:105959200-105970400	Strong transcription	Dnd41	blood
26	chr11:105959400-105970200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr11:105959400-105970200	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr11:105959600-105967200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr11:105959800-105962800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr11:105959800-105970200	Weak transcription	Small Intestine	intestine
31	chr11:105959800-105970400	Weak transcription	Fetal Brain Male	brain
32	chr11:105960200-105966400	Weak transcription	Rectal Smooth Muscle	rectum
33	chr11:105960200-105967800	Weak transcription	Fetal Heart	heart
34	chr11:105961000-105962600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr11:105961000-105968600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr11:105961000-105969000	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr11:105961000-105969400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr11:105961000-105969600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr11:105961000-105970800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr11:105961000-105970800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr11:105961200-105967000	Strong transcription	K562	blood
42	chr11:105961200-105969200	Strong transcription	Fetal Thymus	thymus
43	chr11:105961200-105970200	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr11:105961200-105970400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr11:105961400-105962600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr11:105961400-105968400	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr11:105961400-105968400	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr11:105961400-105968800	Strong transcription	H1 Cell Line	embryonic stem cell
49	chr11:105961400-105968800	Strong transcription	Primary T cells from cord blood	blood
50	chr11:105961400-105969000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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