Variant report

Variant	rs1111615
Chromosome Location	chr3:99410162-99410163
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12485299	0.83[CHB][hapmap]
rs12488843	0.86[ASN][1000 genomes]
rs1492343	0.83[CHB][hapmap]
rs1610263	1.00[CHD][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs1610265	0.92[CHB][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2036984	0.92[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4346581	0.89[YRI][hapmap]
rs4536867	0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4928143	0.83[CHB][hapmap]
rs4928214	1.00[ASW][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap]
rs4928220	0.81[CHB][hapmap]
rs9821563	0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9833844	0.96[ASN][1000 genomes]
rs9834254	0.96[ASN][1000 genomes]
rs9836385	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.89[YRI][hapmap];1.00[ASN][1000 genomes]
rs9842935	0.89[YRI][hapmap]
rs9858145	0.92[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9872469	1.00[ASW][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1111615	CLDND1	cis	cerebellum	SCAN
rs1111615	IFT46	trans	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99394000-99426600	Weak transcription	Stomach Smooth Muscle	stomach
2	chr3:99397200-99411000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr3:99397600-99419200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr3:99397600-99432000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:99397800-99418000	Weak transcription	NHLF	lung
6	chr3:99402200-99410200	Genic enhancers	Muscle Satellite Cultured Cells	--
7	chr3:99403600-99424800	Weak transcription	Colon Smooth Muscle	Colon
8	chr3:99403800-99418200	Weak transcription	Ovary	ovary
9	chr3:99404200-99413400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr3:99406400-99411600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr3:99407000-99419200	Weak transcription	Adipose Nuclei	Adipose
12	chr3:99407600-99418800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr3:99408000-99410200	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr3:99408200-99410200	Enhancers	NHDF-Ad	bronchial
15	chr3:99408200-99413000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr3:99408800-99412800	Strong transcription	Osteobl	bone
17	chr3:99408800-99413400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr3:99409200-99413000	Strong transcription	HSMM	muscle
19	chr3:99409200-99418800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr3:99409600-99411400	Strong transcription	NHEK	skin
21	chr3:99409600-99411600	Strong transcription	NH-A	brain
22	chr3:99409800-99410200	Enhancers	Left Ventricle	heart
23	chr3:99409800-99410400	Genic enhancers	Aorta	Aorta
24	chr3:99409800-99411800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr3:99409800-99412200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr3:99409800-99415200	Strong transcription	HUVEC	blood vessel
27	chr3:99410000-99410200	Enhancers	Psoas Muscle	Psoas

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