Variant report

Variant	rs2026604
Chromosome Location	chr1:153408831-153408832
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:153407654..153409258-chr1:153416471..153419018,2	K562	blood:
2	chr1:153401442..153403093-chr1:153408398..153410070,2	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1024274	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs10888561	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10888563	0.82[ASN][1000 genomes]
rs10888564	0.82[ASN][1000 genomes]
rs10888565	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs10888566	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs10888567	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs1326290	0.86[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap]
rs1409366	0.86[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap]
rs1555885	0.86[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap]
rs2038927	0.86[CHB][hapmap]
rs2148713	0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs2986208	0.86[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs2986213	0.86[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs3006435	0.86[ASN][1000 genomes]
rs3006436	0.86[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs4240869	0.86[ASN][1000 genomes]
rs4845349	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845547	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs6587740	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs715754	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs715755	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7535089	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs913057	0.84[CHB][hapmap];0.89[JPT][hapmap];0.82[YRI][hapmap]
rs983844	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
2	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
3	nsv533877	chr1:152923645-153468131	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv1002705	chr1:153307852-153525589	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
5	nsv831603	chr1:153405842-153576143	Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	148 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2026604	CRNN	cis	cerebellum	SCAN
rs2026604	PSMB4	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153404000-153413800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:153407600-153409600	Enhancers	K562	blood
3	chr1:153408800-153409600	Enhancers	Monocytes-CD14+_RO01746	blood

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