Variant report

Variant	rs1242073
Chromosome Location	chr3:143369778-143369779
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1242049	0.85[EUR][1000 genomes]
rs1242065	0.83[CEU][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];0.81[JPT][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1242066	0.83[CEU][hapmap];0.81[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1242067	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1242068	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1242070	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1242074	0.83[CHD][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.95[MEX][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1242075	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1242077	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1242079	0.81[JPT][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs13101180	0.83[ASN][1000 genomes]
rs2360865	0.92[CHD][hapmap];0.81[JPT][hapmap]
rs56891906	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6762408	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[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	nsv949288	chr3:142793323-143585882	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv829745	chr3:143278512-143405626	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1242073	OR2T8	trans	parietal	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143328200-143376200	Weak transcription	Ovary	ovary
2	chr3:143351600-143369800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr3:143354200-143373600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr3:143354200-143374000	Weak transcription	Esophagus	oesophagus
5	chr3:143358400-143371200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr3:143361400-143373400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr3:143363400-143371200	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr3:143363400-143372800	Weak transcription	Brain Anterior Caudate	brain
9	chr3:143363400-143373800	Weak transcription	Brain Cingulate Gyrus	brain
10	chr3:143363400-143373800	Weak transcription	Brain Hippocampus Middle	brain
11	chr3:143363400-143377600	Weak transcription	NHDF-Ad	bronchial
12	chr3:143363600-143375400	Weak transcription	Fetal Thymus	thymus
13	chr3:143363600-143377800	Weak transcription	Adipose Nuclei	Adipose
14	chr3:143363600-143379000	Weak transcription	Fetal Muscle Leg	muscle
15	chr3:143363800-143373800	Weak transcription	HSMMtube	muscle
16	chr3:143365200-143370800	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr3:143365800-143371200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr3:143367400-143390400	Weak transcription	Brain Substantia Nigra	brain
19	chr3:143367600-143373200	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr3:143367600-143375400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr3:143368200-143370600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr3:143368200-143370600	Weak transcription	Liver	Liver
23	chr3:143368200-143372600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr3:143368600-143370600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr3:143368600-143371000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr3:143368800-143372200	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr3:143369000-143369800	Strong transcription	Primary B cells from cord blood	blood
28	chr3:143369000-143370200	Strong transcription	Duodenum Smooth Muscle	Duodenum
29	chr3:143369000-143370400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr3:143369000-143370800	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr3:143369000-143371200	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr3:143369000-143371800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr3:143369200-143370200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr3:143369400-143370200	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr3:143369400-143370200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr3:143369400-143370400	Weak transcription	Primary T cells from cord blood	blood
37	chr3:143369400-143374600	Weak transcription	Lung	lung
38	chr3:143369600-143369800	Enhancers	ES-I3 Cell Line	embryonic stem cell
39	chr3:143369600-143369800	Genic enhancers	Fetal Lung	lung
40	chr3:143369600-143369800	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr3:143369600-143370200	Enhancers	Primary monocytes fromperipheralblood	blood
42	chr3:143369600-143370200	Enhancers	Primary hematopoietic stem cells short term culture	blood
43	chr3:143369600-143370200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr3:143369600-143372000	Weak transcription	Skeletal Muscle Male	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links