Variant report

Variant	rs853184
Chromosome Location	chr5:142640901-142640902
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:142640359..142641884-chr5:142784509..142786617,2	K562	blood:
2	chr5:142634982..142637716-chr5:142639568..142643122,4	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ARHGAP26-6	chr5:142640409-142640920	NONHSAT104348

Variant related genes	Relation type
ENSG00000113580	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10052957	1.00[JPT][hapmap]
rs10482614	0.87[EUR][1000 genomes]
rs10515522	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs11747997	0.91[ASN][1000 genomes]
rs11749561	1.00[JPT][hapmap]
rs1438732	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1635475	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs174048	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs174050	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1837262	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1866388	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs190488	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2043840	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs258748	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs258750	1.00[JPT][hapmap]
rs258751	1.00[ASN][1000 genomes]
rs258752	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs258753	0.85[JPT][hapmap]
rs258757	0.82[ASN][1000 genomes]
rs258813	1.00[JPT][hapmap]
rs258814	1.00[ASN][1000 genomes]
rs2918415	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2918416	1.00[JPT][hapmap]
rs2918417	1.00[JPT][hapmap]
rs2918418	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2918419	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2963148	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2963149	1.00[JPT][hapmap]
rs2963150	0.95[ASN][1000 genomes]
rs2963151	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs2963154	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs33380	0.95[ASN][1000 genomes]
rs33381	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs33382	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs33389	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55817235	0.84[EUR][1000 genomes]
rs56150733	0.84[EUR][1000 genomes]
rs61752263	0.83[EUR][1000 genomes]
rs6188	1.00[JPT][hapmap]
rs6194	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6196	0.94[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6861962	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs712189	1.00[CHB][hapmap];0.86[JPT][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72801029	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72801054	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72801080	0.83[EUR][1000 genomes]
rs72801090	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72801096	0.85[EUR][1000 genomes]
rs852977	1.00[JPT][hapmap]
rs852978	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs852979	0.98[ASN][1000 genomes]
rs852982	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs852984	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs853154	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs853156	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs853157	1.00[CHB][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs853176	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs853177	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs853178	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs853179	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs853180	0.83[ASW][hapmap]
rs853182	1.00[ASN][1000 genomes]
rs860457	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs860458	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs860465	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs862489	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs864082	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs864355	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs865482	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9324918	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1825941	chr5:142568715-142728031	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	esv33748	chr5:142638267-142699595	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs853184	STK32A	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:142629600-142641600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr5:142630000-142641000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr5:142638000-142641400	Weak transcription	HSMM	muscle
4	chr5:142638800-142641200	Weak transcription	Small Intestine	intestine
5	chr5:142640400-142642200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr5:142640400-142643600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr5:142640600-142641400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr5:142640600-142642400	Enhancers	NHEK	skin
9	chr5:142640600-142642600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr5:142640600-142643400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr5:142640600-142643400	Enhancers	HMEC	breast
12	chr5:142640800-142641200	Enhancers	Pancreatic Islets	Pancreatic Islet
13	chr5:142640800-142641600	Weak transcription	K562	blood
14	chr5:142640800-142643200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr5:142640800-142643400	Enhancers	NHLF	lung

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