Variant report

Variant	rs12157450
Chromosome Location	chr22:31473048-31473049
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10427701	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10854603	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11705177	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11705250	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11705313	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11705319	0.87[EUR][1000 genomes]
rs11705369	0.85[EUR][1000 genomes]
rs11705396	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12158536	0.85[YRI][hapmap]
rs12165471	0.97[ASN][1000 genomes]
rs12168052	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs12170984	0.95[ASN][1000 genomes]
rs12330058	0.94[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.82[MEX][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs13057068	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2006301	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];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2240430	0.84[CHD][hapmap]
rs35060453	0.95[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs5753433	0.84[CEU][hapmap]
rs5753434	0.84[CEU][hapmap]
rs5753436	0.84[CEU][hapmap]
rs5994365	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5994366	1.00[JPT][hapmap]
rs5994368	0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs5994370	1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs5997863	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5997864	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5997866	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5997871	0.87[ASN][1000 genomes]
rs5997872	0.80[ASW][hapmap];0.84[CEU][hapmap];0.84[CHD][hapmap];0.83[TSI][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs715297	1.00[JPT][hapmap]
rs7284593	1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7285683	1.00[JPT][hapmap];0.81[LWK][hapmap]
rs7291565	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7292038	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7292982	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs736901	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];0.90[EUR][1000 genomes]
rs9619166	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9619167	1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9621175	0.95[AFR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv9896	chr22:31369204-31513933	Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	nsv524366	chr22:31440703-31480069	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv829173	chr22:31450043-31543956	Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	esv20214	chr22:31461316-31474644	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	esv1000178	chr22:31461678-31474550	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv914975	chr22:31466083-31514477	Active TSS Flanking Active TSS Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12157450	HSCB	cis	parietal	SCAN
rs12157450	SEZ6L	cis	parietal	SCAN
rs12157450	SEC14L4	cis	cerebellum	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31465800-31475000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr22:31469800-31476400	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr22:31469800-31476400	Weak transcription	HUVEC	blood vessel
4	chr22:31470200-31475000	Weak transcription	Spleen	Spleen
5	chr22:31471400-31476600	Weak transcription	Left Ventricle	heart
6	chr22:31472000-31476400	Weak transcription	HSMMtube	muscle
7	chr22:31472200-31474200	Weak transcription	Osteobl	bone
8	chr22:31472200-31475400	Weak transcription	Lung	lung
9	chr22:31472200-31476200	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr22:31472200-31476400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr22:31472400-31473800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr22:31472400-31473800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr22:31472400-31473800	Weak transcription	Esophagus	oesophagus
14	chr22:31472400-31473800	Weak transcription	Placenta	Placenta
15	chr22:31472400-31474200	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr22:31472400-31474200	Weak transcription	HSMM	muscle
17	chr22:31472400-31474200	Weak transcription	NHEK	skin
18	chr22:31472400-31474400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr22:31472400-31474400	Weak transcription	Stomach Mucosa	stomach
20	chr22:31472400-31475000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr22:31472400-31475000	Weak transcription	Fetal Muscle Trunk	muscle
22	chr22:31472400-31475200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr22:31472400-31476400	Weak transcription	Ovary	ovary
24	chr22:31472400-31476600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr22:31472400-31476600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr22:31472400-31476600	Weak transcription	Psoas Muscle	Psoas
27	chr22:31472600-31473600	Weak transcription	Fetal Intestine Large	intestine
28	chr22:31472600-31473800	Weak transcription	Fetal Intestine Small	intestine
29	chr22:31472600-31474200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr22:31472600-31474200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr22:31472600-31474200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr22:31472600-31474200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr22:31472600-31474200	Weak transcription	Fetal Muscle Leg	muscle
34	chr22:31472600-31474200	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr22:31472600-31475000	Weak transcription	Colonic Mucosa	Colon
36	chr22:31472600-31476200	Weak transcription	Fetal Lung	lung
37	chr22:31472600-31476400	Weak transcription	Adipose Nuclei	Adipose
38	chr22:31472600-31476400	Weak transcription	Right Ventricle	heart
39	chr22:31472600-31476400	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr22:31472600-31476400	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr22:31472600-31476400	Weak transcription	NHDF-Ad	bronchial
42	chr22:31472600-31476600	Weak transcription	Right Atrium	heart
43	chr22:31472600-31476600	Weak transcription	NHLF	lung
44	chr22:31473000-31474200	Weak transcription	Fetal Stomach	stomach

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