Variant report

Variant	rs7332871
Chromosome Location	chr13:38230987-38230988
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1003062	0.80[CHB][hapmap];0.82[CHD][hapmap];0.83[LWK][hapmap];0.81[YRI][hapmap]
rs1570608	0.92[CEU][hapmap]
rs1570609	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1570612	0.85[ASW][hapmap];0.80[CHB][hapmap];0.82[CHD][hapmap];0.83[LWK][hapmap];0.88[YRI][hapmap]
rs1924289	0.88[CHB][hapmap]
rs2025407	0.83[CHB][hapmap]
rs2957215	0.82[CHB][hapmap]
rs2957218	0.83[CHB][hapmap]
rs2985167	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2985170	0.81[CHB][hapmap]
rs4450268	0.83[CHB][hapmap]
rs4603421	0.86[CHB][hapmap]
rs4943527	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4943528	1.00[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7331553	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7336008	0.83[CHB][hapmap]
rs7337173	0.83[CHB][hapmap]
rs7337477	0.83[CHB][hapmap]
rs7338118	0.84[YRI][hapmap]
rs7338239	0.83[CHB][hapmap]
rs7984226	0.85[ASW][hapmap];0.80[CHB][hapmap];0.82[CHD][hapmap];0.84[YRI][hapmap]
rs7996934	0.80[CHB][hapmap];0.84[YRI][hapmap]
rs7997809	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9532099	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs9566246	0.83[CHB][hapmap]
rs9566247	0.83[CHB][hapmap]
rs9566248	0.83[CHB][hapmap]
rs9566249	0.83[CHB][hapmap]
rs9576332	0.83[CHB][hapmap]
rs9594224	0.83[CHB][hapmap]
rs9594226	0.83[CHB][hapmap]
rs9603244	0.88[CHB][hapmap]
rs9603245	0.83[CHB][hapmap]
rs9603246	0.83[CHB][hapmap]

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
rs7332871	SPG20	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:38211400-38275600	Weak transcription	Stomach Smooth Muscle	stomach
2	chr13:38221600-38239600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr13:38221800-38231400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr13:38221800-38233200	Weak transcription	Ovary	ovary
5	chr13:38221800-38239400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr13:38224400-38233200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr13:38225600-38246600	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr13:38228000-38238200	Weak transcription	Left Ventricle	heart
9	chr13:38228800-38233600	Enhancers	NHDF-Ad	bronchial
10	chr13:38229800-38232400	Enhancers	Hela-S3	cervix
11	chr13:38229800-38232600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr13:38229800-38232600	Enhancers	Muscle Satellite Cultured Cells	--
13	chr13:38229800-38233200	Enhancers	Osteobl	bone
14	chr13:38230000-38231000	Enhancers	HUVEC	blood vessel
15	chr13:38230000-38231400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr13:38230000-38231800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr13:38230000-38231800	Enhancers	HMEC	breast
18	chr13:38230000-38231800	Enhancers	NHEK	skin
19	chr13:38230000-38233200	Enhancers	NHLF	lung
20	chr13:38230200-38231000	Enhancers	A549	lung
21	chr13:38230400-38231400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr13:38230400-38231400	Flanking Active TSS	NH-A	brain
23	chr13:38230400-38231600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr13:38230400-38232200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr13:38230600-38232000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr13:38230800-38231000	Enhancers	Aorta	Aorta
27	chr13:38230800-38232200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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