Variant report

Variant	rs4896461
Chromosome Location	chr6:139807622-139807623
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	chr6:139805921..139807747-chr6:139809317..139811941,2	K562	blood:
2	chr6:139689617..139691791-chr6:139807268..139808961,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HECA-5	chr6:139807573-139807752	NONHSAT115255

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1468708	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1468709	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2908513	0.84[JPT][hapmap]
rs3010286	0.96[CHD][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.88[ASN][1000 genomes]
rs3010288	0.91[ASN][1000 genomes]
rs4896463	0.88[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4896464	0.80[AMR][1000 genomes]
rs6570344	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6907607	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6916887	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6923416	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[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];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6926031	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7770257	0.81[AMR][1000 genomes]
rs9376420	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[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];0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9403080	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4896461	ARVCF	trans	parietal	SCAN
rs4896461	CHRNB2	trans	cerebellum	SCAN
rs4896461	FUCA2	cis	parietal	SCAN

Chromatin state (count:16 , 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	chr6:139806400-139807800	Enhancers	HepG2	liver
4	chr6:139806600-139807800	Enhancers	Fetal Stomach	stomach
5	chr6:139807000-139807800	Enhancers	Fetal Kidney	kidney
6	chr6:139807000-139811200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr6:139807200-139807800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr6:139807200-139807800	Enhancers	Stomach Smooth Muscle	stomach
9	chr6:139807200-139808000	Flanking Active TSS	Liver	Liver
10	chr6:139807400-139807800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr6:139807400-139807800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr6:139807400-139807800	Enhancers	Lung	lung
13	chr6:139807400-139807800	Enhancers	Ovary	ovary
14	chr6:139807400-139807800	Enhancers	Pancreas	Pancrea
15	chr6:139807400-139807800	Enhancers	GM12878-XiMat	blood
16	chr6:139807600-139807800	Enhancers	HUES6 Cell Line	embryonic stem cell

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