Variant report

Variant	rs1339552
Chromosome Location	chr9:16848790-16848791
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10283446	0.87[ASN][1000 genomes]
rs10810648	0.86[ASN][1000 genomes]
rs10810650	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10810652	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10810655	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10810657	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10962650	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10962668	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12345776	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12350739	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1416742	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2153271	1.00[CEU][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.80[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3927680	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4644350	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62541919	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7040151	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024799	chr9:16631890-17431827	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv892650	chr9:16696187-16950860	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv892651	chr9:16816755-16869240	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv892652	chr9:16843128-16958312	Bivalent Enhancer Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
5	nsv892653	chr9:16848790-16895610	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1339552	CNTLN	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16829200-16852800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:16829800-16864200	Weak transcription	NH-A	brain
3	chr9:16831000-16859600	Weak transcription	HSMM	muscle
4	chr9:16831200-16852600	Weak transcription	Fetal Lung	lung
5	chr9:16831200-16863400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr9:16831200-16864400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr9:16833800-16863800	Weak transcription	NHLF	lung
8	chr9:16834600-16852600	Weak transcription	Fetal Stomach	stomach
9	chr9:16836200-16864400	Weak transcription	NHDF-Ad	bronchial
10	chr9:16838800-16852000	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr9:16840400-16852000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr9:16840600-16849400	Weak transcription	Ovary	ovary
13	chr9:16842200-16852000	Weak transcription	Colon Smooth Muscle	Colon
14	chr9:16843000-16853200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr9:16843400-16850600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr9:16845200-16849600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr9:16846000-16851200	Weak transcription	Fetal Muscle Leg	muscle
18	chr9:16846600-16852000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr9:16846600-16852800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr9:16848000-16849400	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr9:16848200-16849000	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr9:16848400-16848800	Enhancers	HUES48 Cell Line	embryonic stem cell
23	chr9:16848400-16852800	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr9:16848600-16852000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr9:16848600-16852600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr9:16848600-16852800	Weak transcription	H1 Cell Line	embryonic stem cell

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