Variant report

Variant	rs40005
Chromosome Location	chr3:138081051-138081052
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	chr3:138079655..138082250-chr3:138142327..138144870,2	K562	blood:
2	chr3:138073894..138077050-chr3:138080713..138083758,3	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1199333	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1199334	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1199335	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1199336	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1199346	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1199347	1.00[ASN][1000 genomes]
rs1201763	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1209710	0.91[CEU][hapmap];0.96[GIH][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs1212469	0.95[ASN][1000 genomes]
rs1308362	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1624314	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs166195	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs166196	1.00[ASN][1000 genomes]
rs1679149	0.86[ASN][1000 genomes]
rs183151	0.90[ASN][1000 genomes]
rs194146	0.86[ASN][1000 genomes]
rs253662	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs253664	0.96[GIH][hapmap]
rs253666	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs40412	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs42761	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4437085	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs774373	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs799328	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs811332	1.00[JPT][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530056	chr3:137312356-138161861	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv877537	chr3:137979007-138215114	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv530057	chr3:138014877-138734390	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv528349	chr3:138025396-138132393	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv1796956	chr3:138051423-138122781	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	esv1848610	chr3:138051423-138133412	Bivalent Enhancer Genic enhancers Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs40005	SR140	cis	cerebellum	SCAN
rs40005	A4GNT	cis	parietal	SCAN
rs40005	GPR172B	trans	parietal	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138068400-138083000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:138068600-138084600	Weak transcription	Gastric	stomach
3	chr3:138068800-138093200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:138069200-138088200	Weak transcription	Fetal Lung	lung
5	chr3:138070000-138096600	Weak transcription	Fetal Brain Male	brain
6	chr3:138070200-138086400	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr3:138071000-138085600	Weak transcription	Brain Germinal Matrix	brain
8	chr3:138071200-138082400	Weak transcription	Spleen	Spleen
9	chr3:138071200-138082800	Weak transcription	Esophagus	oesophagus
10	chr3:138071200-138096600	Weak transcription	Aorta	Aorta
11	chr3:138071600-138086600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr3:138071800-138083400	Weak transcription	Placenta	Placenta
13	chr3:138073800-138084600	Weak transcription	Fetal Intestine Small	intestine
14	chr3:138074200-138095600	Enhancers	Fetal Heart	heart
15	chr3:138074800-138089800	Enhancers	Brain Cingulate Gyrus	brain
16	chr3:138075000-138086400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr3:138075000-138090000	Enhancers	Brain Anterior Caudate	brain
18	chr3:138075400-138087400	Enhancers	Right Atrium	heart
19	chr3:138075600-138081200	Enhancers	Adipose Nuclei	Adipose
20	chr3:138075600-138081600	Enhancers	Brain Hippocampus Middle	brain
21	chr3:138075600-138082800	Enhancers	Left Ventricle	heart
22	chr3:138075600-138089400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
23	chr3:138076000-138086400	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr3:138076000-138108200	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr3:138076400-138082400	Enhancers	Brain Inferior Temporal Lobe	brain
26	chr3:138077000-138083000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr3:138077400-138081800	Enhancers	HepG2	liver
28	chr3:138077800-138082400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr3:138077800-138091600	Enhancers	Right Ventricle	heart
30	chr3:138078200-138081200	Weak transcription	Fetal Kidney	kidney
31	chr3:138078400-138081200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr3:138078600-138086400	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr3:138078600-138100600	Weak transcription	NH-A	brain
34	chr3:138078800-138081800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr3:138078800-138086600	Strong transcription	Fetal Stomach	stomach
36	chr3:138079000-138085400	Weak transcription	Colon Smooth Muscle	Colon
37	chr3:138079400-138081200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr3:138079600-138081600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr3:138079600-138095600	Weak transcription	Fetal Brain Female	brain
40	chr3:138079800-138081800	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr3:138079800-138082800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr3:138079800-138086600	Weak transcription	Osteobl	bone
43	chr3:138080000-138081600	Enhancers	HSMMtube	muscle
44	chr3:138080000-138083000	Weak transcription	Stomach Smooth Muscle	stomach
45	chr3:138080200-138086200	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr3:138080200-138096400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr3:138080400-138081200	Enhancers	Skeletal Muscle Male	skeletal muscle
48	chr3:138080400-138081600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr3:138080400-138082200	Weak transcription	Ovary	ovary
50	chr3:138080400-138082800	Enhancers	Brain Substantia Nigra	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links