Variant report

Variant	rs9460974
Chromosome Location	chr6:24188947-24188948
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10085260	0.81[EUR][1000 genomes]
rs12192874	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12196541	0.91[CHD][hapmap]
rs12197434	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12199816	0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12212062	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12213642	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1856839	0.96[ASN][1000 genomes]
rs2876667	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28990375	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4535539	1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.96[ASN][1000 genomes]
rs6914194	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6914641	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6938792	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs793851	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs793852	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9358755	0.85[CEU][hapmap]
rs9467072	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9467073	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9467075	0.93[ASN][1000 genomes]
rs9467076	1.00[JPT][hapmap];0.89[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	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	nsv601146	chr6:24166233-24215665	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9460974	DCDC2	cis	parietal	SCAN
rs9460974	HIST1H1E	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24153800-24200800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:24172800-24194800	Weak transcription	Fetal Intestine Large	intestine
3	chr6:24177800-24198400	Weak transcription	A549	lung
4	chr6:24181400-24189600	Strong transcription	HepG2	liver
5	chr6:24184200-24195200	Weak transcription	Pancreas	Pancrea
6	chr6:24184600-24195000	Weak transcription	Fetal Intestine Small	intestine
7	chr6:24186600-24196000	Weak transcription	Fetal Kidney	kidney
8	chr6:24187000-24189400	Weak transcription	Fetal Brain Male	brain

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