Variant report

Variant	rs1433219
Chromosome Location	chr4:124706056-124706057
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10002832	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10003021	0.93[EUR][1000 genomes]
rs10028082	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10031024	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10031632	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10031894	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10518306	0.80[CEU][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[EUR][1000 genomes]
rs11098722	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11729742	0.93[EUR][1000 genomes]
rs1425403	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1425404	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1425406	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1425407	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17007176	1.00[JPT][hapmap]
rs17007241	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17007305	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1895754	0.93[EUR][1000 genomes]
rs2194866	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28361300	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28361543	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28376823	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28470742	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28493674	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28595508	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28670181	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28699481	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28805878	0.93[EUR][1000 genomes]
rs4833290	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4833291	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4833292	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4833935	0.93[EUR][1000 genomes]
rs4833939	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4833942	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4833945	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4833946	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4833947	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4833948	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4833949	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4833952	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57927362	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57978274	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59468019	0.93[EUR][1000 genomes]
rs6821590	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6827679	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6828406	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6847358	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72929724	0.93[EUR][1000 genomes]
rs72929781	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7659116	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7668462	0.93[EUR][1000 genomes]
rs7677587	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7691744	0.93[EUR][1000 genomes]
rs7692299	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7699549	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9631736	0.87[EUR][1000 genomes]
rs9992459	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34581	chr4:124271321-125247395	Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1001751	chr4:124693346-124733305	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
3	esv2754745	chr4:124698055-124770865	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1433219	QRFPR	cis	parietal	SCAN
rs1433219	TRPC3	cis	parietal	SCAN
rs1433219	PRNP	trans	lymphoblastoid	seeQTL

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:124694200-124707800	Weak transcription	Pancreas	Pancrea
2	chr4:124698800-124708000	Weak transcription	Right Atrium	heart
3	chr4:124703600-124706400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr4:124703600-124708600	Enhancers	Osteobl	bone
5	chr4:124703600-124710000	Enhancers	NHLF	lung
6	chr4:124703800-124706200	Enhancers	NHDF-Ad	bronchial
7	chr4:124703800-124710200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr4:124704000-124708200	Weak transcription	Stomach Mucosa	stomach
9	chr4:124704000-124708400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr4:124704000-124709800	Enhancers	Muscle Satellite Cultured Cells	--
11	chr4:124704600-124708400	Enhancers	HSMM	muscle
12	chr4:124704600-124708800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr4:124704600-124709200	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr4:124704600-124709200	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr4:124704600-124709200	Enhancers	iPS-20b Cell Line	embryonic stem cell
16	chr4:124704600-124710000	Enhancers	Fetal Muscle Leg	muscle
17	chr4:124704800-124706200	Enhancers	Colon Smooth Muscle	Colon
18	chr4:124704800-124706600	Enhancers	Rectal Smooth Muscle	rectum
19	chr4:124704800-124707400	Weak transcription	Psoas Muscle	Psoas
20	chr4:124704800-124708000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr4:124704800-124709000	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr4:124704800-124709800	Enhancers	Fetal Stomach	stomach
23	chr4:124704800-124710000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr4:124705000-124706600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr4:124705000-124708000	Weak transcription	Ovary	ovary
26	chr4:124705000-124710200	Enhancers	Fetal Lung	lung
27	chr4:124705200-124706600	Weak transcription	Stomach Smooth Muscle	stomach
28	chr4:124705200-124706800	Weak transcription	Aorta	Aorta
29	chr4:124705400-124706200	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr4:124705400-124706600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr4:124705400-124706600	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr4:124705400-124707600	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr4:124705600-124706600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr4:124705600-124706800	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr4:124705600-124706800	Weak transcription	Fetal Heart	heart
36	chr4:124705800-124706400	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr4:124705800-124706800	Weak transcription	Adipose Nuclei	Adipose
38	chr4:124705800-124706800	Weak transcription	HSMMtube	muscle
39	chr4:124706000-124706400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr4:124706000-124707800	Weak transcription	NH-A	brain

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