Variant report

Variant	rs1508588
Chromosome Location	chr1:91964229-91964230
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZBTB33	chr1:91964062-91964388	HepG2	liver:	n/a	n/a
2	MAFK	chr1:91963040-91970259	HepG2	liver:	n/a	chr1:91966021-91966035 chr1:91968577-91968588
3	FOSL2	chr1:91964033-91964781	HepG2	liver:	n/a	n/a
4	JUND	chr1:91963265-91969107	HepG2	liver:	n/a	chr1:91966158-91966170 chr1:91967689-91967697 chr1:91966078-91966087 chr1:91966604-91966613 chr1:91968312-91968321 chr1:91968136-91968145
5	FOSL2	chr1:91962979-91969220	HepG2	liver:	n/a	chr1:91966158-91966170 chr1:91967689-91967697 chr1:91966078-91966087 chr1:91966604-91966613 chr1:91968312-91968321 chr1:91968136-91968145
6	JUN	chr1:91964050-91964465	HepG2	liver:	n/a	chr1:91964269-91964282
7	ARID3A	chr1:91963133-91969929	HepG2	liver:	n/a	chr1:91968303-91968319

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HFM1-1	chr1:91964072-91964760	XLOC_000916

Variant related genes	Relation type
CDC7	TF binding region

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10399689	0.90[EUR][1000 genomes]
rs10399810	0.90[EUR][1000 genomes]
rs10399813	0.90[EUR][1000 genomes]
rs10399814	1.00[CEU][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes]
rs10493849	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10493850	0.95[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.94[EUR][1000 genomes]
rs10493851	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes]
rs10518494	0.84[AMR][1000 genomes]
rs10782953	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10874758	0.95[EUR][1000 genomes]
rs10874782	1.00[CEU][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes]
rs11164837	0.84[AMR][1000 genomes]
rs11164877	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11164899	0.87[EUR][1000 genomes]
rs11164913	0.87[EUR][1000 genomes]
rs11164915	0.85[EUR][1000 genomes]
rs12024529	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12025632	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12027099	0.86[EUR][1000 genomes]
rs12028436	0.90[EUR][1000 genomes]
rs12029889	0.86[EUR][1000 genomes]
rs12031239	0.85[EUR][1000 genomes]
rs12035234	0.86[EUR][1000 genomes]
rs12035345	0.87[EUR][1000 genomes]
rs12036176	0.87[EUR][1000 genomes]
rs12036298	0.85[EUR][1000 genomes]
rs12046667	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12057283	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12070660	0.90[EUR][1000 genomes]
rs12758662	0.88[EUR][1000 genomes]
rs12759236	0.87[EUR][1000 genomes]
rs12759724	0.87[EUR][1000 genomes]
rs13447523	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1531232	0.87[EUR][1000 genomes]
rs1876264	1.00[CEU][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes]
rs2219394	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs2297709	0.93[EUR][1000 genomes]
rs2893175	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35504045	0.85[EUR][1000 genomes]
rs4658225	0.88[EUR][1000 genomes]
rs499574	0.82[CEU][hapmap]
rs745732	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][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	nsv949516	chr1:91644418-92109261	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv1009560	chr1:91897078-92270781	Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1508588	CDC7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:91956600-91965800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr1:91962000-91965600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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