Variant report

Variant	rs10057004
Chromosome Location	chr5:60041034-60041035
allele	C/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	POLR2A	chr5:60040201-60041145	K562	blood:	n/a	n/a

Variant related genes	Relation type
KRT8P31	TF binding region

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10050803	0.89[CEU][hapmap];0.86[JPT][hapmap]
rs10054744	0.83[EUR][1000 genomes]
rs10058456	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs10069929	0.83[EUR][1000 genomes]
rs10440618	0.83[EUR][1000 genomes]
rs10805370	1.00[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs10939860	0.81[CEU][hapmap]
rs10939863	0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.81[ASN][1000 genomes]
rs12522801	0.81[CEU][hapmap]
rs12655515	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs13153359	0.93[CHB][hapmap];0.84[JPT][hapmap];0.89[ASN][1000 genomes]
rs13186761	0.84[ASN][1000 genomes]
rs13358053	0.93[CHB][hapmap];0.89[ASN][1000 genomes]
rs1456742	0.86[CEU][hapmap]
rs1456743	0.86[CEU][hapmap]
rs1960479	0.82[EUR][1000 genomes]
rs2085412	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2409796	0.91[ASN][1000 genomes]
rs28766005	0.82[ASN][1000 genomes]
rs3899221	0.82[EUR][1000 genomes]
rs4235480	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4307050	0.93[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs4400080	0.83[EUR][1000 genomes]
rs4458532	0.91[ASN][1000 genomes]
rs4524466	0.85[CEU][hapmap]
rs4577661	0.82[EUR][1000 genomes]
rs4700385	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4700387	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57521726	0.81[ASN][1000 genomes]
rs6449483	1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs6449484	0.93[CHB][hapmap]
rs6449485	0.81[ASN][1000 genomes]
rs6449489	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6874072	1.00[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs702564	0.92[CHB][hapmap];0.84[JPT][hapmap];0.89[ASN][1000 genomes]
rs7704338	1.00[CHB][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs7708864	0.85[AMR][1000 genomes]
rs7719611	1.00[CHB][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs7719726	0.87[CHB][hapmap]
rs7730342	0.86[CEU][hapmap]
rs897672	1.00[CHB][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492277	chr5:59905195-60180834	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv462198	chr5:59969015-60116613	Strong transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv598298	chr5:59969015-60116613	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1023403	chr5:59969534-60079822	Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv508362	chr5:59990308-60050894	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv934153	chr5:60004982-60309751	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	esv2763456	chr5:60007355-60151767	Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
8	nsv1026190	chr5:60020156-60148535	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
9	nsv537769	chr5:60020156-60148535	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
10	esv2752073	chr5:60034475-60136626	Weak transcription Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10057004	DEPDC1B	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60036200-60044800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:60037400-60047600	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr5:60040800-60066600	Weak transcription	Fetal Intestine Small	intestine

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