Variant report

Variant	rs253664
Chromosome Location	chr3:138113353-138113354
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1199328	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1199333	0.89[CEU][hapmap];0.96[GIH][hapmap];0.85[MEX][hapmap];0.96[TSI][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1199334	0.89[CEU][hapmap];0.96[GIH][hapmap];0.85[MEX][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes]
rs1199335	0.90[CEU][hapmap];0.96[GIH][hapmap];0.85[MEX][hapmap];0.96[TSI][hapmap];0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1199336	0.89[CEU][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1199346	0.80[AMR][1000 genomes]
rs1199347	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1201763	0.96[GIH][hapmap];1.00[LWK][hapmap];0.80[AMR][1000 genomes]
rs1209710	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1212469	0.95[EUR][1000 genomes]
rs13082471	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1308362	0.95[CEU][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1624314	0.89[CEU][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs166195	0.88[CEU][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs166196	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1679149	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1720825	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1720827	1.00[ASN][1000 genomes]
rs183151	0.90[EUR][1000 genomes]
rs194146	0.91[EUR][1000 genomes]
rs253662	0.95[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs253666	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs40005	0.96[GIH][hapmap]
rs42761	0.96[GIH][hapmap];0.80[AMR][1000 genomes]
rs4346503	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4437085	0.80[AMR][1000 genomes]
rs4678416	0.92[EUR][1000 genomes]
rs6809480	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs774373	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs799328	0.89[CEU][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs808934	1.00[ASN][1000 genomes]
rs811332	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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
12	nsv526089	chr3:138106698-138122781	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs253664	A4GNT	cis	parietal	SCAN
rs253664	LOC126536	trans	parietal	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138090400-138119400	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr3:138097600-138116000	Weak transcription	Aorta	Aorta
3	chr3:138097600-138116600	Weak transcription	Brain Germinal Matrix	brain
4	chr3:138101200-138115000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:138101400-138123000	Weak transcription	Fetal Lung	lung
6	chr3:138101600-138120400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr3:138108000-138115800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr3:138109000-138116800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr3:138109200-138116000	Weak transcription	Fetal Brain Female	brain
10	chr3:138109200-138116800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr3:138109200-138119600	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr3:138109400-138113600	Weak transcription	Fetal Muscle Trunk	muscle
13	chr3:138109400-138114000	Weak transcription	Right Atrium	heart
14	chr3:138109400-138114400	Weak transcription	Brain Hippocampus Middle	brain
15	chr3:138109400-138114800	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr3:138109400-138114800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr3:138109400-138114800	Weak transcription	Fetal Stomach	stomach
18	chr3:138109400-138115200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr3:138109400-138115400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr3:138109400-138115800	Weak transcription	Fetal Muscle Leg	muscle
21	chr3:138109400-138115800	Weak transcription	Gastric	stomach
22	chr3:138109400-138116800	Weak transcription	Stomach Smooth Muscle	stomach
23	chr3:138109400-138119600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:138109600-138114400	Weak transcription	Brain Anterior Caudate	brain
25	chr3:138109600-138114800	Weak transcription	Brain Cingulate Gyrus	brain
26	chr3:138109600-138115200	Weak transcription	Ovary	ovary
27	chr3:138109600-138115800	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr3:138109600-138117200	Weak transcription	Pancreas	Pancrea
29	chr3:138109600-138120600	Weak transcription	Colon Smooth Muscle	Colon
30	chr3:138109600-138123000	Weak transcription	Rectal Smooth Muscle	rectum
31	chr3:138109600-138124400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr3:138109800-138114200	Weak transcription	Lung	lung
33	chr3:138109800-138115200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr3:138109800-138115400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr3:138109800-138117200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr3:138109800-138118800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr3:138109800-138119600	Weak transcription	Placenta	Placenta
38	chr3:138109800-138123000	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr3:138109800-138124800	Weak transcription	NHLF	lung
40	chr3:138109800-138131400	Weak transcription	NHDF-Ad	bronchial
41	chr3:138110200-138114200	Weak transcription	Brain Angular Gyrus	brain
42	chr3:138110200-138114400	Weak transcription	Brain Substantia Nigra	brain
43	chr3:138110200-138116200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr3:138110200-138117200	Weak transcription	Osteobl	bone
45	chr3:138110200-138120200	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr3:138110200-138121400	Weak transcription	NH-A	brain
47	chr3:138110400-138114800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr3:138110400-138116400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr3:138111200-138114600	Strong transcription	HSMM	muscle
50	chr3:138111400-138116200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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