Variant report

Variant	rs1242074
Chromosome Location	chr3:143367503-143367504
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:143367249..143368125-chr3:143481961..143482742,5	MCF-7	breast:
2	chr3:143367217..143368245-chr3:143392896..143393845,7	MCF-7	breast:
3	chr3:143366241..143367963-chr3:143375379..143377183,2	K562	blood:
4	chr3:143367288..143367898-chr3:143392977..143393650,2	MCF-7	breast:

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1242065	0.91[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1242066	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1242067	0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1242068	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1242070	0.82[CHD][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1242073	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	0.83[CEU][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1242077	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1242079	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6762408	0.80[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs7613679	0.83[MKK][hapmap];0.87[YRI][hapmap];0.85[ASN][1000 genomes]
rs9873621	0.85[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
rs1242074	OR2T8	trans	parietal	SCAN

Chromatin state (count:35 , 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	chr3:143357800-143369000	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr3:143358200-143369000	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr3:143358400-143371200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr3:143360200-143369600	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr3:143361400-143373400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr3:143363400-143369000	Weak transcription	Primary B cells from cord blood	blood
11	chr3:143363400-143371200	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr3:143363400-143372800	Weak transcription	Brain Anterior Caudate	brain
13	chr3:143363400-143373800	Weak transcription	Brain Cingulate Gyrus	brain
14	chr3:143363400-143373800	Weak transcription	Brain Hippocampus Middle	brain
15	chr3:143363400-143377600	Weak transcription	NHDF-Ad	bronchial
16	chr3:143363600-143368600	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr3:143363600-143375400	Weak transcription	Fetal Thymus	thymus
18	chr3:143363600-143377800	Weak transcription	Adipose Nuclei	Adipose
19	chr3:143363600-143379000	Weak transcription	Fetal Muscle Leg	muscle
20	chr3:143363800-143369000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr3:143363800-143373800	Weak transcription	HSMMtube	muscle
22	chr3:143364000-143369000	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr3:143364000-143369600	Weak transcription	Fetal Lung	lung
24	chr3:143365200-143370800	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr3:143365400-143368600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr3:143365800-143371200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr3:143367000-143367800	Enhancers	Placenta	Placenta
28	chr3:143367200-143367600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr3:143367200-143367800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
30	chr3:143367200-143368000	Enhancers	HUES6 Cell Line	embryonic stem cell
31	chr3:143367400-143367600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
32	chr3:143367400-143367800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
33	chr3:143367400-143367800	Enhancers	K562	blood
34	chr3:143367400-143369200	Weak transcription	Primary T cells from cord blood	blood
35	chr3:143367400-143390400	Weak transcription	Brain Substantia Nigra	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links