Variant report

Variant	rs9548010
Chromosome Location	chr13:38244897-38244898
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11147663	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12583344	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12585258	1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17056196	0.89[JPT][hapmap]
rs17056424	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs17197663	0.89[JPT][hapmap]
rs17199750	0.89[JPT][hapmap]
rs17201866	0.89[JPT][hapmap]
rs17257154	0.89[JPT][hapmap]
rs17257328	0.89[JPT][hapmap]
rs17261242	0.91[GIH][hapmap]
rs1924302	0.89[JPT][hapmap]
rs1924303	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3829364	0.89[JPT][hapmap]
rs4512969	0.89[JPT][hapmap]
rs4628831	0.89[JPT][hapmap]
rs4943526	1.00[CHB][hapmap]
rs7338082	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9548007	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9548009	1.00[CHB][hapmap]
rs9548011	0.94[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9548013	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9548017	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9603242	0.94[CEU][hapmap];0.88[JPT][hapmap];0.89[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	nsv948975	chr13:37281203-38280430	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	esv34109	chr13:37843819-38276391	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv1045716	chr13:37952062-38394595	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv915901	chr13:38199035-39032633	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9548010	CSNK1A1L	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:38211400-38275600	Weak transcription	Stomach Smooth Muscle	stomach
2	chr13:38225600-38246600	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr13:38231800-38255000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr13:38234000-38256000	Weak transcription	Ovary	ovary
5	chr13:38240200-38246400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr13:38240200-38250000	Weak transcription	NH-A	brain
7	chr13:38240600-38245800	Weak transcription	Osteobl	bone
8	chr13:38240600-38254600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr13:38240600-38255400	Weak transcription	NHLF	lung
10	chr13:38240600-38256600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr13:38241000-38255400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr13:38244400-38249800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr13:38244800-38255400	Weak transcription	NHDF-Ad	bronchial

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