Variant report

Variant	rs1468708
Chromosome Location	chr6:139808046-139808047
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:139795343..139797706-chr6:139807680..139810551,2	K562	blood:
2	chr6:139793534..139795180-chr6:139807994..139810598,2	MCF-7	breast:
3	chr6:139689617..139691791-chr6:139807268..139808961,2	K562	blood:

Variant related genes	Relation type
ENSG00000238099	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10872516	0.81[AMR][1000 genomes]
rs11155070	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1468709	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2908513	0.84[JPT][hapmap]
rs3010286	0.96[CHD][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.87[ASN][1000 genomes]
rs3010288	0.90[ASN][1000 genomes]
rs4896461	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4896463	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4896464	0.80[AMR][1000 genomes]
rs6570344	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6907607	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6916887	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6923416	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6926031	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7770257	0.81[AMR][1000 genomes]
rs9376420	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9376421	0.81[AMR][1000 genomes]
rs9376422	0.81[AMR][1000 genomes]
rs9376423	0.81[AMR][1000 genomes]
rs9389689	0.83[AMR][1000 genomes]
rs9399281	0.92[YRI][hapmap]
rs9399282	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9403080	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9403082	0.81[AMR][1000 genomes]
rs9403083	0.81[AMR][1000 genomes]
rs9403084	0.88[JPT][hapmap];0.81[AMR][1000 genomes]
rs9495502	0.84[JPT][hapmap];0.81[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869066	chr6:139777114-140639695	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1468708	FUCA2	cis	parietal	SCAN
rs1468708	CHRNB2	trans	cerebellum	SCAN
rs1468708	ARVCF	trans	parietal	SCAN
rs1468708	ISLR	trans	brain	seeQTL

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:139804000-139818200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:139804600-139810800	Weak transcription	K562	blood
3	chr6:139807000-139811200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr6:139807800-139808800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:139807800-139809400	Weak transcription	HepG2	liver
6	chr6:139807800-139811000	Weak transcription	Pancreas	Pancrea
7	chr6:139807800-139811600	Weak transcription	Fetal Kidney	kidney
8	chr6:139808000-139810200	Enhancers	Liver	Liver

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