Variant report

Variant	rs13058342
Chromosome Location	chr22:34238831-34238832
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1009385	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.84[JPT][hapmap];0.96[MEX][hapmap];0.90[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11089633	0.90[JPT][hapmap]
rs11705248	0.82[MEX][hapmap]
rs12483818	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];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13053314	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16993143	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16993180	0.92[CHD][hapmap];0.82[GIH][hapmap];0.84[JPT][hapmap];0.83[MEX][hapmap];0.85[ASN][1000 genomes]
rs2267293	0.83[MEX][hapmap]
rs2267294	0.83[MEX][hapmap]
rs2267299	0.81[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2267301	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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2267308	0.83[CHD][hapmap];0.90[GIH][hapmap]
rs2283950	0.90[JPT][hapmap];0.82[AMR][1000 genomes]
rs34573078	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3819667	0.94[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3827344	0.82[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];0.84[JPT][hapmap];0.87[MEX][hapmap];0.85[ASN][1000 genomes]
rs4820120	1.00[CEU][hapmap];0.92[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67503539	0.86[ASN][1000 genomes]
rs67714362	0.85[ASN][1000 genomes]
rs68063018	0.85[ASN][1000 genomes]
rs762836	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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
14	esv3343210	chr22:34236744-34404210	Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13058342	LARGE	cis	Artery Tibial	GTEx
rs13058342	HMGXB4	cis	parietal	SCAN

Chromatin state (count:49 , 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	chr22:34232000-34240400	Weak transcription	Esophagus	oesophagus
4	chr22:34232000-34244200	Weak transcription	Stomach Smooth Muscle	stomach
5	chr22:34232200-34239200	Enhancers	Fetal Heart	heart
6	chr22:34232200-34240200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr22:34232200-34240200	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr22:34232600-34246800	Weak transcription	Gastric	stomach
9	chr22:34234200-34240200	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr22:34234200-34243600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr22:34234200-34245200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr22:34234600-34244400	Weak transcription	Lung	lung
13	chr22:34235000-34240400	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr22:34235200-34239400	Enhancers	H1 Cell Line	embryonic stem cell
15	chr22:34235200-34240200	Weak transcription	Fetal Lung	lung
16	chr22:34235200-34242000	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr22:34235400-34240200	Weak transcription	Rectal Smooth Muscle	rectum
18	chr22:34235400-34240200	Weak transcription	Right Atrium	heart
19	chr22:34235600-34240200	Weak transcription	Colon Smooth Muscle	Colon
20	chr22:34235600-34240200	Weak transcription	Fetal Intestine Small	intestine
21	chr22:34235800-34239000	Enhancers	iPS-20b Cell Line	embryonic stem cell
22	chr22:34236200-34240200	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr22:34236200-34240200	Weak transcription	Fetal Intestine Large	intestine
24	chr22:34236600-34239200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr22:34236800-34239600	Enhancers	Left Ventricle	heart
26	chr22:34237400-34239600	Enhancers	Primary B cells from peripheral blood	blood
27	chr22:34237600-34239000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr22:34237800-34239000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr22:34237800-34239000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr22:34237800-34239200	Enhancers	NHDF-Ad	bronchial
31	chr22:34237800-34239600	Weak transcription	Ovary	ovary
32	chr22:34237800-34240200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr22:34237800-34240200	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr22:34237800-34240200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr22:34237800-34240200	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr22:34237800-34242800	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr22:34237800-34244200	Weak transcription	Osteobl	bone
38	chr22:34237800-34246000	Weak transcription	Right Ventricle	heart
39	chr22:34237800-34246800	Weak transcription	Psoas Muscle	Psoas
40	chr22:34237800-34247200	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr22:34238000-34239000	Active TSS	GM12878-XiMat	blood
42	chr22:34238000-34240400	Weak transcription	HepG2	liver
43	chr22:34238200-34240200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr22:34238200-34240200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr22:34238400-34239000	Enhancers	HUES64 Cell Line	embryonic stem cell
46	chr22:34238400-34240200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr22:34238400-34249000	Weak transcription	Aorta	Aorta
48	chr22:34238800-34240000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr22:34238800-34240200	Weak transcription	NHLF	lung

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