Variant report

Variant	rs1538999
Chromosome Location	chr9:18498954-18498955
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1006022	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10217409	0.94[ASN][1000 genomes]
rs10217753	0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.89[ASN][1000 genomes]
rs10453192	0.82[EUR][1000 genomes]
rs10733354	0.83[EUR][1000 genomes]
rs10738511	0.83[EUR][1000 genomes]
rs10810973	0.90[EUR][1000 genomes]
rs10810974	0.81[CHD][hapmap];0.80[GIH][hapmap];0.91[JPT][hapmap]
rs1147795	0.96[YRI][hapmap]
rs11793923	0.92[CEU][hapmap];0.92[YRI][hapmap];0.91[EUR][1000 genomes]
rs12339807	0.86[ASN][1000 genomes]
rs12340914	0.86[ASN][1000 genomes]
rs1281352	0.91[EUR][1000 genomes]
rs1329720	0.91[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap]
rs1417037	0.89[CEU][hapmap];0.88[YRI][hapmap];0.83[EUR][1000 genomes]
rs16936779	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs1832638	0.81[EUR][1000 genomes]
rs1888068	0.89[CEU][hapmap];0.81[YRI][hapmap];0.84[EUR][1000 genomes]
rs1888069	0.92[CEU][hapmap];0.86[YRI][hapmap];0.85[EUR][1000 genomes]
rs2149875	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2153415	0.93[ASW][hapmap];0.92[CEU][hapmap];0.92[LWK][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2153416	1.00[ASW][hapmap];0.92[CEU][hapmap];0.82[CHD][hapmap];0.90[LWK][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2277160	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34619899	0.85[ASN][1000 genomes]
rs3898100	0.82[EUR][1000 genomes]
rs4246142	0.81[EUR][1000 genomes]
rs4246143	0.83[EUR][1000 genomes]
rs4590536	0.83[EUR][1000 genomes]
rs4961651	0.88[EUR][1000 genomes]
rs4961652	0.92[CEU][hapmap];0.84[CHD][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.91[EUR][1000 genomes]
rs4961653	0.87[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4961654	0.83[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6475219	0.82[EUR][1000 genomes]
rs6475220	0.92[CEU][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];0.82[JPT][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs6475221	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7019399	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs7032393	0.83[EUR][1000 genomes]
rs7036515	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7046502	0.83[EUR][1000 genomes]
rs7856703	0.92[CEU][hapmap];0.82[CHD][hapmap];0.90[LWK][hapmap];0.98[TSI][hapmap];0.84[YRI][hapmap];0.89[EUR][1000 genomes]
rs7864622	0.95[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs7864727	0.95[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs7867766	0.92[CEU][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491807	chr9:18243672-19009770	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv525659	chr9:18288212-19009041	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1019127	chr9:18288271-18996288	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv892688	chr9:18385143-18551247	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv1029449	chr9:18414752-18829127	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
6	nsv540077	chr9:18414752-18829127	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
7	nsv1030931	chr9:18414752-18903530	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
8	nsv892689	chr9:18485434-18537444	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv892690	chr9:18485434-18592374	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1538999	CNTLN	cis	cerebellum	SCAN
rs1538999	FREM1	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:18490400-18509400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:18493800-18502400	Weak transcription	Ovary	ovary
3	chr9:18494000-18501000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr9:18494400-18500400	Genic enhancers	Osteobl	bone
5	chr9:18495400-18499600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr9:18495400-18499800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr9:18495400-18500000	Weak transcription	NHEK	skin
8	chr9:18495400-18513200	Weak transcription	HUVEC	blood vessel
9	chr9:18495600-18499800	Weak transcription	HMEC	breast
10	chr9:18496800-18507000	Weak transcription	NHLF	lung
11	chr9:18497000-18501000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr9:18497000-18501000	Enhancers	NHDF-Ad	bronchial
13	chr9:18497000-18502800	Enhancers	Fetal Lung	lung
14	chr9:18497200-18499000	Weak transcription	HSMMtube	muscle
15	chr9:18497200-18500000	Weak transcription	Stomach Smooth Muscle	stomach
16	chr9:18498000-18501200	Weak transcription	Fetal Stomach	stomach
17	chr9:18498200-18499000	Weak transcription	Rectal Smooth Muscle	rectum
18	chr9:18498200-18500000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr9:18498200-18500000	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr9:18498200-18501800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr9:18498400-18499200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr9:18498400-18499200	Enhancers	Fetal Muscle Leg	muscle
23	chr9:18498400-18500400	Enhancers	Right Ventricle	heart
24	chr9:18498600-18499400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr9:18498600-18499400	Enhancers	Duodenum Smooth Muscle	Duodenum
26	chr9:18498600-18500000	Strong transcription	HSMM	muscle
27	chr9:18498600-18500400	Enhancers	Colon Smooth Muscle	Colon
28	chr9:18498800-18499000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr9:18498800-18499200	Active TSS	Fetal Brain Male	brain
30	chr9:18498800-18499400	Enhancers	NH-A	brain
31	chr9:18498800-18499600	Flanking Active TSS	Fetal Heart	heart

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