Variant report

Variant	rs1308362
Chromosome Location	chr3:138103927-138103928
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1199328	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1199333	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1199334	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1199335	0.95[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];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1199336	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1199346	0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1199347	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1201763	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1209710	1.00[ASW][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs1212469	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13082471	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1624314	0.94[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs166195	0.94[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs166196	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1679149	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1720825	0.95[CEU][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs183151	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs194146	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs253662	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]
rs253664	0.95[CEU][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs253666	0.89[AMR][1000 genomes]
rs40005	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs40412	0.95[ASN][1000 genomes]
rs42761	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4346503	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4437085	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4678416	0.94[EUR][1000 genomes]
rs6809480	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs774373	1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs799328	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs811332	1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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
10	nsv460864	chr3:138100539-138194435	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
11	nsv591853	chr3:138100539-138194435	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1308362	A4GNT	cis	parietal	SCAN
rs1308362	LOC126536	trans	parietal	SCAN

Chromatin state (count:62 , 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	chr3:138081600-138108200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:138090400-138119400	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr3:138094000-138104800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr3:138097600-138116000	Weak transcription	Aorta	Aorta
6	chr3:138097600-138116600	Weak transcription	Brain Germinal Matrix	brain
7	chr3:138098200-138104200	Enhancers	Fetal Heart	heart
8	chr3:138099200-138104000	Enhancers	Right Ventricle	heart
9	chr3:138099600-138105200	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr3:138099800-138104000	Enhancers	Left Ventricle	heart
11	chr3:138099800-138104200	Enhancers	Placenta	Placenta
12	chr3:138099800-138104200	Enhancers	Right Atrium	heart
13	chr3:138100000-138104000	Genic enhancers	HSMMtube	muscle
14	chr3:138101200-138105000	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr3:138101200-138106000	Weak transcription	Fetal Stomach	stomach
16	chr3:138101200-138115000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr3:138101400-138106400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr3:138101400-138108000	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr3:138101400-138108400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr3:138101400-138123000	Weak transcription	Fetal Lung	lung
21	chr3:138101600-138104200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr3:138101600-138107800	Weak transcription	Osteobl	bone
23	chr3:138101600-138108000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr3:138101600-138108200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr3:138101600-138108200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr3:138101600-138108200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr3:138101600-138120400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr3:138101800-138108000	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr3:138101800-138108200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr3:138101800-138108200	Weak transcription	Pancreas	Pancrea
31	chr3:138101800-138108400	Weak transcription	Fetal Muscle Leg	muscle
32	chr3:138101800-138108400	Weak transcription	Rectal Smooth Muscle	rectum
33	chr3:138101800-138108600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr3:138102000-138107000	Strong transcription	HSMM	muscle
35	chr3:138102000-138108200	Weak transcription	Esophagus	oesophagus
36	chr3:138102000-138108200	Weak transcription	Fetal Muscle Trunk	muscle
37	chr3:138102200-138105200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr3:138102200-138106600	Weak transcription	Fetal Brain Female	brain
39	chr3:138102400-138108000	Weak transcription	Psoas Muscle	Psoas
40	chr3:138102600-138104000	Enhancers	K562	blood
41	chr3:138102600-138106200	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr3:138102600-138108000	Weak transcription	Colon Smooth Muscle	Colon
43	chr3:138102600-138108200	Weak transcription	Stomach Smooth Muscle	stomach
44	chr3:138102600-138109200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr3:138103000-138108000	Weak transcription	Ovary	ovary
46	chr3:138103200-138108000	Weak transcription	Brain Hippocampus Middle	brain
47	chr3:138103400-138104000	Enhancers	HepG2	liver
48	chr3:138103400-138108600	Weak transcription	NHEK	skin
49	chr3:138103600-138104200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr3:138103600-138107400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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