Variant report

Variant	rs870601
Chromosome Location	chr6:24261060-24261061
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10806986	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10946689	0.94[CHB][hapmap];0.87[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11754080	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12055879	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12197973	0.85[ASN][1000 genomes]
rs12216513	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1578349	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2274305	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2296539	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3789228	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4712817	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6456601	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs793843	0.85[EUR][1000 genomes]
rs807697	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs807698	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs807700	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs807701	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs807722	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9295620	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9379649	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9379650	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9393541	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029930	chr6:23481989-24289948	Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv427746	chr6:24221299-24305709	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	esv3381453	chr6:24260899-24261339	Weak transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs870601	HIST1H4A	cis	parietal	SCAN
rs870601	PRSS16	cis	parietal	SCAN
rs870601	HIST1H2BO	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24232000-24263000	Weak transcription	Fetal Intestine Small	intestine
2	chr6:24243800-24270000	Weak transcription	Fetal Kidney	kidney
3	chr6:24252400-24261600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:24258000-24261600	Weak transcription	HepG2	liver
5	chr6:24259800-24263000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr6:24260800-24261400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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