Variant report

Variant	rs17476063
Chromosome Location	chr1:223016406-223016407
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1132369	0.87[ASN][1000 genomes]
rs1132371	0.87[ASN][1000 genomes]
rs11487817	0.82[LWK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs11487861	0.82[LWK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs11597	0.85[AFR][1000 genomes]
rs17163510	0.85[AFR][1000 genomes]
rs17163518	0.85[AFR][1000 genomes]
rs17475774	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs17534774	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs17535032	0.87[ASN][1000 genomes]
rs17535137	0.87[ASN][1000 genomes]
rs17535305	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs28362013	0.95[CEU][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs34074917	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34151467	0.87[ASN][1000 genomes]
rs34299243	0.87[ASN][1000 genomes]
rs34596963	0.83[AMR][1000 genomes]
rs34682656	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34764163	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34791822	0.87[ASN][1000 genomes]
rs34873092	0.90[AMR][1000 genomes]
rs34984199	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35197173	0.87[ASN][1000 genomes]
rs35270996	0.82[ASN][1000 genomes]
rs35271605	0.85[AFR][1000 genomes]
rs35530937	0.85[AFR][1000 genomes]
rs35979308	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs36044931	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs36083483	0.97[EUR][1000 genomes]
rs4609435	0.95[CEU][hapmap];0.97[EUR][1000 genomes]
rs61838112	0.97[EUR][1000 genomes]
rs61838114	0.97[EUR][1000 genomes]
rs61839585	0.85[AFR][1000 genomes]
rs61839589	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61839593	0.85[AFR][1000 genomes]
rs61839600	0.87[ASN][1000 genomes]
rs61839601	0.87[ASN][1000 genomes]
rs61839602	0.87[ASN][1000 genomes]
rs61839607	0.85[AFR][1000 genomes]
rs61839609	0.85[AFR][1000 genomes]
rs61840264	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs61840265	0.90[AMR][1000 genomes]
rs61840266	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs66597772	0.90[AMR][1000 genomes]
rs71644708	0.87[ASN][1000 genomes]
rs71644709	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999185	chr1:222500725-223278032	Strong transcription Enhancers Weak transcription Flanking Active TSS 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 miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv535304	chr1:222500725-223278032	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv1012537	chr1:222755091-223512243	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv873206	chr1:222985197-223124916	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17476063	RP11-452F19.3	cis	Esophagus Muscularis	GTEx
rs17476063	CAPN2	cis	lymphoblastoid	seeQTL
rs17476063	DISP1	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:222989400-223026800	Weak transcription	Fetal Muscle Leg	muscle
2	chr1:222990400-223027400	Weak transcription	Primary B cells from cord blood	blood
3	chr1:222991800-223017200	Weak transcription	Aorta	Aorta
4	chr1:222997000-223016600	Weak transcription	Primary hematopoietic stem cells	blood
5	chr1:223002200-223017000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr1:223002600-223019800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr1:223007200-223017200	Weak transcription	Fetal Lung	lung
8	chr1:223007800-223016800	Weak transcription	Fetal Intestine Small	intestine
9	chr1:223007800-223017400	Weak transcription	Colon Smooth Muscle	Colon
10	chr1:223008000-223017000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:223010800-223027600	Weak transcription	Primary B cells from peripheral blood	blood
12	chr1:223012800-223017000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr1:223013000-223016800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr1:223013000-223016800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr1:223013600-223030800	Weak transcription	Ovary	ovary
16	chr1:223015800-223017400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr1:223016000-223017400	Enhancers	Duodenum Mucosa	Duodenum
18	chr1:223016000-223018400	Enhancers	Stomach Mucosa	stomach
19	chr1:223016200-223017600	Enhancers	Rectal Smooth Muscle	rectum
20	chr1:223016400-223016800	Weak transcription	Fetal Intestine Large	intestine
21	chr1:223016400-223018200	Active TSS	Pancreatic Islets	Pancreatic Islet

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