Variant report

Variant	rs253662
Chromosome Location	chr3:138097313-138097314
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1199328	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1199333	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1199334	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1199335	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1199336	0.94[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1199346	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1199347	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1201763	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1209710	0.96[GIH][hapmap];0.85[LWK][hapmap];0.82[AMR][1000 genomes]
rs1212469	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13082471	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1308362	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1624314	0.94[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs166195	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs166196	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1679149	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1720825	0.95[CEU][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs183151	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs194146	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs253664	0.95[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.82[YRI][hapmap]
rs253666	0.82[YRI][hapmap];0.82[AMR][1000 genomes]
rs40005	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs40412	1.00[ASN][1000 genomes]
rs42761	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4346503	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4437085	1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4678416	0.96[EUR][1000 genomes]
rs6809480	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs774373	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs799328	0.94[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs811332	1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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
7	esv1797142	chr3:138087467-138122781	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	esv1845560	chr3:138087467-138133412	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	esv3447663	chr3:138096329-138273034	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs253662	A4GNT	cis	parietal	SCAN
rs253662	LOC126536	trans	parietal	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138076000-138108200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:138078600-138100600	Weak transcription	NH-A	brain
3	chr3:138081600-138108200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:138083000-138100400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:138083200-138100600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:138085200-138100000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr3:138086200-138100400	Weak transcription	HepG2	liver
8	chr3:138086800-138100600	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr3:138087200-138100000	Weak transcription	Pancreas	Pancrea
10	chr3:138087200-138100600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr3:138089200-138100000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr3:138089200-138100800	Weak transcription	Fetal Lung	lung
13	chr3:138089400-138100000	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr3:138089400-138100000	Weak transcription	Brain Angular Gyrus	brain
15	chr3:138089400-138102400	Weak transcription	Spleen	Spleen
16	chr3:138089600-138097600	Weak transcription	Brain Substantia Nigra	brain
17	chr3:138089600-138100200	Weak transcription	Lung	lung
18	chr3:138090400-138119400	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr3:138091000-138098000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr3:138091200-138100400	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr3:138091400-138100800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr3:138091600-138098600	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr3:138091800-138098000	Strong transcription	HSMM	muscle
24	chr3:138093400-138097600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr3:138093600-138100400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr3:138093800-138100000	Weak transcription	Colon Smooth Muscle	Colon
27	chr3:138093800-138100400	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr3:138094000-138104800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr3:138094400-138100200	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr3:138094600-138097400	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr3:138094600-138099000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr3:138094600-138100600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr3:138094800-138100200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr3:138095000-138098000	Strong transcription	Fetal Muscle Leg	muscle
35	chr3:138095200-138097600	Strong transcription	Brain Germinal Matrix	brain
36	chr3:138095400-138097400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr3:138095600-138097400	Genic enhancers	Fetal Heart	heart
38	chr3:138095600-138098000	Strong transcription	Fetal Brain Female	brain
39	chr3:138095800-138098800	Strong transcription	HSMMtube	muscle
40	chr3:138096000-138097400	Enhancers	Psoas Muscle	Psoas
41	chr3:138096000-138097600	Strong transcription	Fetal Stomach	stomach
42	chr3:138096000-138097600	Genic enhancers	Left Ventricle	heart
43	chr3:138096000-138098200	Enhancers	Placenta	Placenta
44	chr3:138096200-138097600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr3:138096200-138097600	Enhancers	Right Atrium	heart
46	chr3:138096200-138097800	Strong transcription	Fetal Muscle Trunk	muscle
47	chr3:138096400-138097400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
48	chr3:138096400-138097600	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr3:138096400-138097800	Genic enhancers	Brain Anterior Caudate	brain
50	chr3:138096600-138097400	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links