Variant report

Variant	rs17455509
Chromosome Location	chr3:43037177-43037178
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:43032109..43034625-chr3:43036764..43039846,3	K562	blood:
2	chr3:43034830..43037319-chr3:43041912..43044241,2	K562	blood:

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10212191	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs10510736	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs13080201	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13093968	1.00[LWK][hapmap]
rs17390473	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17455760	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17469719	1.00[ASW][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.82[TSI][hapmap]
rs2001682	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs2062517	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs2948619	0.81[JPT][hapmap]
rs34100558	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3953390	0.88[ASN][1000 genomes]
rs531888	0.81[CHB][hapmap];0.83[CHD][hapmap];0.84[JPT][hapmap]
rs532792	0.84[JPT][hapmap]
rs55701670	0.86[ASN][1000 genomes]
rs55848724	0.84[ASN][1000 genomes]
rs56292257	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs644534	0.81[CHB][hapmap];0.83[CHD][hapmap];0.84[JPT][hapmap]
rs66603383	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67186096	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6764648	0.83[CHB][hapmap]
rs6783218	0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6792817	0.97[ASN][1000 genomes]
rs6793871	0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6794402	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs6806427	0.81[CHB][hapmap]
rs6807814	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs704903	0.90[CEU][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs7616750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7619227	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7624799	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];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7633590	0.81[CHB][hapmap];1.00[CHD][hapmap]
rs7634125	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7637698	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7643433	0.93[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs834177	0.81[CHB][hapmap]
rs872126	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs9311332	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs9812262	0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9821320	0.81[CHB][hapmap];1.00[CHD][hapmap]
rs9848904	0.81[CHB][hapmap];0.83[CHD][hapmap];0.84[JPT][hapmap]
rs9863179	0.89[ASN][1000 genomes]
rs9872107	0.97[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	nsv460522	chr3:42967597-43175207	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv590149	chr3:42967597-43175207	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh 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
3	nsv460523	chr3:43025986-43063406	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv590150	chr3:43025986-43063406	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17455509	CCDC13	cis	parietal	SCAN
rs17455509	ZNF621	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:43023000-43037800	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr3:43030800-43037800	Weak transcription	Liver	Liver
3	chr3:43032600-43040800	Weak transcription	Placenta	Placenta
4	chr3:43033400-43038200	Weak transcription	Pancreas	Pancrea
5	chr3:43033400-43039600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr3:43033600-43038200	Weak transcription	Fetal Muscle Trunk	muscle
7	chr3:43033800-43037200	Weak transcription	Fetal Muscle Leg	muscle
8	chr3:43033800-43037600	Weak transcription	Stomach Smooth Muscle	stomach
9	chr3:43034000-43038000	Weak transcription	Adipose Nuclei	Adipose
10	chr3:43034000-43038000	Weak transcription	Ovary	ovary
11	chr3:43034000-43038200	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr3:43034000-43038400	Weak transcription	Esophagus	oesophagus
13	chr3:43034200-43037400	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr3:43034200-43037600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr3:43034200-43037600	Weak transcription	Brain Angular Gyrus	brain
16	chr3:43034200-43037600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr3:43034200-43043400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr3:43034400-43037200	Weak transcription	Brain Hippocampus Middle	brain
19	chr3:43034600-43037400	Weak transcription	Brain Substantia Nigra	brain
20	chr3:43036000-43039200	Enhancers	Brain Anterior Caudate	brain
21	chr3:43036200-43038000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr3:43036800-43038800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr3:43037000-43037200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:43037000-43038400	Enhancers	Right Atrium	heart
25	chr3:43037000-43039200	Enhancers	Brain Cingulate Gyrus	brain

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