Variant report

Variant	rs7984226
Chromosome Location	chr13:38245603-38245604
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1003062	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10161932	0.93[CEU][hapmap];0.91[JPT][hapmap];0.90[TSI][hapmap]
rs10507456	0.82[LWK][hapmap];0.81[MKK][hapmap]
rs1413005	0.81[GIH][hapmap]
rs1535775	0.94[CEU][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1570609	0.80[CHB][hapmap];0.96[YRI][hapmap]
rs1570612	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17056378	1.00[CEU][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1886165	1.00[CEU][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1924296	0.81[CEU][hapmap];0.91[JPT][hapmap];0.90[TSI][hapmap]
rs1924306	0.81[CEU][hapmap];0.90[JPT][hapmap];0.86[TSI][hapmap]
rs1977278	0.87[CEU][hapmap];0.91[JPT][hapmap];0.89[TSI][hapmap]
rs2025405	0.87[CEU][hapmap];0.91[JPT][hapmap];0.90[TSI][hapmap]
rs2181747	0.85[CHB][hapmap]
rs2985167	0.80[CHB][hapmap];0.82[CHD][hapmap]
rs3812842	0.81[CEU][hapmap];0.90[JPT][hapmap]
rs4943528	0.85[ASW][hapmap];0.84[YRI][hapmap]
rs7319022	0.81[EUR][1000 genomes]
rs7319663	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7320832	0.81[CEU][hapmap];0.91[JPT][hapmap];0.86[TSI][hapmap]
rs7329459	0.88[CEU][hapmap];0.96[EUR][1000 genomes]
rs7330467	0.81[EUR][1000 genomes]
rs7332871	0.85[ASW][hapmap];0.80[CHB][hapmap];0.82[CHD][hapmap];0.84[YRI][hapmap]
rs7335776	0.80[EUR][1000 genomes]
rs7338118	1.00[CEU][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7338244	0.87[CEU][hapmap];0.91[JPT][hapmap];0.90[TSI][hapmap]
rs7996934	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7997809	0.85[ASW][hapmap];0.80[CHB][hapmap];0.82[CHD][hapmap];0.87[LWK][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes]
rs8001743	0.85[CHB][hapmap]
rs9576310	0.81[CEU][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap]
rs9576319	0.80[EUR][1000 genomes]
rs9594229	0.85[CHB][hapmap]
rs9603240	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9603241	1.00[CEU][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9603247	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]

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
rs7984226	SPG20	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:38211400-38275600	Weak transcription	Stomach Smooth Muscle	stomach
2	chr13:38225600-38246600	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr13:38231800-38255000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr13:38234000-38256000	Weak transcription	Ovary	ovary
5	chr13:38240200-38246400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr13:38240200-38250000	Weak transcription	NH-A	brain
7	chr13:38240600-38245800	Weak transcription	Osteobl	bone
8	chr13:38240600-38254600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr13:38240600-38255400	Weak transcription	NHLF	lung
10	chr13:38240600-38256600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr13:38241000-38255400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr13:38244400-38249800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr13:38244800-38255400	Weak transcription	NHDF-Ad	bronchial

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