Variant report

Variant	rs6656979
Chromosome Location	chr1:159782181-159782182
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:159778155..159780944-chr1:159782160..159785920,3	K562	blood:
2	chr1:159781040..159782914-chr1:159845764..159848603,2	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11265280	0.93[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11265282	0.92[CEU][hapmap];0.95[GIH][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11585836	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11590202	0.88[ASN][1000 genomes]
rs11590961	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12083595	0.82[JPT][hapmap];0.92[ASN][1000 genomes]
rs12083967	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12088352	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12090961	0.93[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2494495	0.85[EUR][1000 genomes]
rs2494519	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2501343	0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs4301626	0.81[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4443889	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4656851	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55650803	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55739401	0.81[AMR][1000 genomes]
rs57198275	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58024147	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58240276	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59414252	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60205880	0.85[AMR][1000 genomes]
rs6656168	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6657365	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6659704	0.93[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6672434	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6692290	0.93[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7512164	0.93[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.85[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	nsv1005195	chr1:159452759-159910337	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv521503	chr1:159762120-159795478	Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6656979	HAPLN2	cis	cerebellum	SCAN
rs6656979	NES	cis	parietal	SCAN
rs6656979	COPA	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:159774800-159796000	Weak transcription	Right Atrium	heart
2	chr1:159775800-159793400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr1:159776800-159784200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr1:159779400-159783200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr1:159779600-159794800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr1:159780000-159785200	Weak transcription	Spleen	Spleen

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