Variant report

Variant	rs16949545
Chromosome Location	chr13:94824146-94824147
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10129085	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10161943	0.89[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs1328821	0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs1328822	0.92[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs17196050	0.85[EUR][1000 genomes]
rs4142203	0.84[CHB][hapmap]
rs475933	0.85[EUR][1000 genomes]
rs494817	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs497636	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs497836	0.96[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs502029	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs504825	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs541134	0.96[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs543744	0.96[CEU][hapmap];0.81[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap];0.81[TSI][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs588792	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs589258	0.96[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs591981	0.95[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];0.81[JPT][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs603741	0.96[CEU][hapmap];0.81[CHB][hapmap];0.94[CHD][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs605033	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61570339	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs618895	0.87[CEU][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs622908	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs637086	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs638325	0.85[EUR][1000 genomes]
rs6492696	0.81[CHB][hapmap]
rs685049	0.95[CEU][hapmap];0.81[CHB][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7991937	0.92[CHD][hapmap]
rs9524350	0.85[CHB][hapmap]
rs9561507	0.80[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs9589918	0.80[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs9589922	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][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	nsv933807	chr13:94187158-94845505	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv948455	chr13:94451368-94988900	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv916640	chr13:94521959-95101443	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv533063	chr13:94560362-95101443	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv430599	chr13:94699399-94934930	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv933263	chr13:94711183-94897124	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv1051276	chr13:94745995-94872494	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv526048	chr13:94767311-94880219	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv562754	chr13:94770794-94895346	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16949545	CLDN10	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:94814800-94825400	Weak transcription	Fetal Intestine Small	intestine
2	chr13:94821200-94824200	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr13:94821800-94824400	Enhancers	iPS-18 Cell Line	embryonic stem cell
4	chr13:94822000-94824200	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr13:94822000-94824400	Enhancers	H1 Cell Line	embryonic stem cell
6	chr13:94822000-94824400	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr13:94822000-94824400	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr13:94822000-94824600	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr13:94822000-94825600	Weak transcription	Aorta	Aorta
10	chr13:94822200-94834200	Weak transcription	Fetal Kidney	kidney
11	chr13:94822600-94825000	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr13:94822600-94828600	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr13:94822800-94825000	Weak transcription	HSMM	muscle
14	chr13:94822800-94825000	Weak transcription	NH-A	brain
15	chr13:94823000-94824200	Enhancers	iPS-20b Cell Line	embryonic stem cell
16	chr13:94823200-94824400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr13:94823200-94824600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr13:94823200-94825200	Weak transcription	Fetal Stomach	stomach
19	chr13:94823400-94824200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr13:94823400-94824200	Enhancers	H9 Cell Line	embryonic stem cell
21	chr13:94823400-94825000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr13:94823400-94825000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr13:94823400-94825000	Weak transcription	Osteobl	bone
24	chr13:94823600-94824200	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr13:94823600-94825000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr13:94823600-94825000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr13:94823600-94825000	Weak transcription	Liver	Liver
28	chr13:94824000-94824200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr13:94824000-94824200	Enhancers	Fetal Lung	lung
30	chr13:94824000-94824400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr13:94824000-94825800	Weak transcription	Adipose Nuclei	Adipose

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