Variant report

Variant	rs2240861
Chromosome Location	chr3:42750324-42750325
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:42749483..42751308-chr3:42753064..42754909,2	K562	blood:
2	chr3:42742913..42747022-chr3:42748348..42751882,5	MCF-7	breast:
3	chr3:42746557..42750988-chr3:42768421..42772654,4	K562	blood:

Variant related genes	Relation type
ENSG00000010282	Chromatin interaction
ENSG00000230970	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10461012	0.97[EUR][1000 genomes]
rs10865920	0.95[EUR][1000 genomes]
rs10865921	0.95[EUR][1000 genomes]
rs10865923	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11129969	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11129970	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11709054	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11709500	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11713172	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11717346	0.82[CHD][hapmap];0.90[JPT][hapmap]
rs11915803	0.89[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17074778	0.94[CEU][hapmap];0.86[TSI][hapmap];0.95[EUR][1000 genomes]
rs17238314	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17238798	0.84[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs339664	0.82[CHD][hapmap];0.90[JPT][hapmap]
rs339668	0.82[CHD][hapmap];0.90[JPT][hapmap]
rs339676	0.82[CHD][hapmap];0.90[JPT][hapmap]
rs34110933	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4682856	0.90[CHD][hapmap];0.82[JPT][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes]
rs4682857	0.90[JPT][hapmap]
rs4683336	0.83[CHB][hapmap]
rs55884426	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55904344	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59478814	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59713146	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60049195	0.95[EUR][1000 genomes]
rs60176972	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62246603	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62246606	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62246635	0.85[EUR][1000 genomes]
rs62250113	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62250114	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6442057	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6764909	0.82[CHD][hapmap];0.90[JPT][hapmap]
rs72865716	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9836162	1.00[CEU][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9837412	0.83[CEU][hapmap];0.90[CHB][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9838388	0.94[CEU][hapmap];0.90[EUR][1000 genomes]
rs9880635	0.86[CHB][hapmap];0.90[JPT][hapmap]

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	nsv1013578	chr3:42747858-42817321	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv999713	chr3:42749022-42817321	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2240861	ZNF35	cis	cerebellum	SCAN
rs2240861	LRRC2	cis	cerebellum	SCAN
rs2240861	HHATL	cis	parietal	SCAN
rs2240861	FYCO1	cis	cerebellum	SCAN
rs2240861	EXOSC7	cis	cerebellum	SCAN
rs2240861	HHATL	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42739200-42751800	Weak transcription	Pancreas	Pancrea
2	chr3:42745600-42753000	Weak transcription	Brain Cingulate Gyrus	brain
3	chr3:42745800-42752800	Weak transcription	Brain Angular Gyrus	brain
4	chr3:42746200-42753000	Weak transcription	Brain Anterior Caudate	brain
5	chr3:42746600-42750400	Weak transcription	Spleen	Spleen
6	chr3:42746600-42752800	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr3:42746800-42752800	Weak transcription	Brain Substantia Nigra	brain
8	chr3:42747400-42752800	Weak transcription	Brain Hippocampus Middle	brain
9	chr3:42747600-42751200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr3:42747800-42760200	Weak transcription	Right Atrium	heart
11	chr3:42748800-42752000	Weak transcription	Skeletal Muscle Female	skeletal muscle

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