Variant report

Variant	rs5754714
Chromosome Location	chr22:34235677-34235678
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12484737	0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs16993156	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17809399	1.00[ASW][hapmap];0.97[GIH][hapmap]
rs2018285	0.94[CEU][hapmap];0.83[CHB][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2253063	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2267306	0.95[CHB][hapmap];0.93[CHD][hapmap];0.86[ASN][1000 genomes]
rs2283952	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5749677	0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs5749679	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5749680	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5749682	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5754715	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5754716	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5754717	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5754731	0.89[GIH][hapmap]
rs5999123	1.00[ASW][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap]
rs738949	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv934109	chr22:33722066-34339500	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
2	esv2763261	chr22:33831348-34288389	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1057450	chr22:33928913-34849012	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv914990	chr22:34090440-34373293	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv914991	chr22:34106384-34293516	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1056553	chr22:34116979-34286191	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv914992	chr22:34135007-34283144	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv524156	chr22:34145596-34260738	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv529886	chr22:34153740-34258847	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv1061736	chr22:34178034-34394918	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv544689	chr22:34178034-34394918	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv1066419	chr22:34231732-34553006	Active TSS Genic enhancers Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv544690	chr22:34231732-34553006	Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs5754714	HSCB	cis	parietal	SCAN
rs5754714	CABP7	cis	parietal	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:34226600-34246200	Weak transcription	Duodenum Mucosa	Duodenum
2	chr22:34228800-34240000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr22:34231000-34236000	Enhancers	Skeletal Muscle Female	skeletal muscle
4	chr22:34231400-34236000	Enhancers	Left Ventricle	heart
5	chr22:34231800-34238800	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr22:34232000-34240400	Weak transcription	Esophagus	oesophagus
7	chr22:34232000-34244200	Weak transcription	Stomach Smooth Muscle	stomach
8	chr22:34232200-34239200	Enhancers	Fetal Heart	heart
9	chr22:34232200-34240200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr22:34232200-34240200	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr22:34232600-34237400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr22:34232600-34246800	Weak transcription	Gastric	stomach
13	chr22:34233000-34237400	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr22:34233400-34236000	Enhancers	Ovary	ovary
15	chr22:34233600-34235800	Weak transcription	Psoas Muscle	Psoas
16	chr22:34233800-34235800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr22:34234000-34236600	Weak transcription	Right Ventricle	heart
18	chr22:34234000-34236800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr22:34234200-34240200	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr22:34234200-34243600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr22:34234200-34245200	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr22:34234400-34236000	Enhancers	Aorta	Aorta
23	chr22:34234600-34244400	Weak transcription	Lung	lung
24	chr22:34234800-34237200	Enhancers	GM12878-XiMat	blood
25	chr22:34235000-34236000	Enhancers	H9 Cell Line	embryonic stem cell
26	chr22:34235000-34240400	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr22:34235200-34236000	Enhancers	Fetal Kidney	kidney
28	chr22:34235200-34236000	Enhancers	Pancreas	Pancrea
29	chr22:34235200-34236200	Enhancers	Fetal Intestine Large	intestine
30	chr22:34235200-34237400	Enhancers	HUES64 Cell Line	embryonic stem cell
31	chr22:34235200-34237800	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr22:34235200-34237800	Enhancers	HUES48 Cell Line	embryonic stem cell
33	chr22:34235200-34239400	Enhancers	H1 Cell Line	embryonic stem cell
34	chr22:34235200-34240200	Weak transcription	Fetal Lung	lung
35	chr22:34235200-34242000	Enhancers	iPS-15b Cell Line	embryonic stem cell
36	chr22:34235400-34235800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
37	chr22:34235400-34236000	Enhancers	HepG2	liver
38	chr22:34235400-34236200	Enhancers	HUES6 Cell Line	embryonic stem cell
39	chr22:34235400-34240200	Weak transcription	Rectal Smooth Muscle	rectum
40	chr22:34235400-34240200	Weak transcription	Right Atrium	heart
41	chr22:34235600-34236600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr22:34235600-34237000	Weak transcription	NHLF	lung
43	chr22:34235600-34237200	Weak transcription	NHDF-Ad	bronchial
44	chr22:34235600-34237400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr22:34235600-34237400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr22:34235600-34240200	Weak transcription	Colon Smooth Muscle	Colon
47	chr22:34235600-34240200	Weak transcription	Fetal Intestine Small	intestine

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