Variant report

Variant	rs10010575
Chromosome Location	chr4:75190202-75190203
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CUX1	chr4:75190089-75190327	K562	blood:	n/a	n/a
2	POLR2A	chr4:75176225-75192444	MCF10A-Er-Src	breast:	n/a	n/a
3	RCOR1	chr4:75189977-75190310	K562	blood:	n/a	n/a
4	POLR2A	chr4:75188985-75191022	MCF10A-Er-Src	breast:	n/a	n/a
5	RCOR1	chr4:75189981-75190449	K562	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:75186018..75191874-chr4:75238287..75242590,7	MCF-7	breast:
2	chr4:75189693..75192750-chr4:75229705..75235376,6	K562	blood:
3	chr4:75188724..75190900-chr4:75238906..75240715,2	MCF-7	breast:
4	chr4:75189014..75191731-chr4:75230700..75232890,4	K562	blood:
5	chr4:75190057..75192592-chr4:75257362..75259075,2	K562	blood:
6	chr4:75021640..75024587-chr4:75190198..75192467,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000265720	TF binding region
ENSG00000269559	Chromatin interaction
ENSG00000124882	Chromatin interaction
ENSG00000163738	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10009707	0.84[EUR][1000 genomes]
rs10017409	0.97[TSI][hapmap];0.86[EUR][1000 genomes]
rs10018373	0.84[TSI][hapmap]
rs10023519	0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs10026687	0.83[EUR][1000 genomes]
rs10028285	0.85[EUR][1000 genomes]
rs1037824	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11737662	0.84[TSI][hapmap]
rs11942725	0.86[CEU][hapmap];0.91[EUR][1000 genomes]
rs1246575	0.84[TSI][hapmap]
rs1246578	0.84[TSI][hapmap]
rs1246591	0.84[TSI][hapmap]
rs1265327	0.84[TSI][hapmap]
rs1460016	0.84[TSI][hapmap]
rs16850862	0.86[EUR][1000 genomes]
rs16850883	0.93[CEU][hapmap];0.88[JPT][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16850941	0.84[CEU][hapmap];0.91[EUR][1000 genomes]
rs17232394	0.83[EUR][1000 genomes]
rs17829765	0.87[CEU][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes]
rs2045616	0.82[ASW][hapmap];0.83[CEU][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.84[LWK][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2045617	0.82[CEU][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2061508	0.97[TSI][hapmap];0.83[EUR][1000 genomes]
rs28539097	0.84[EUR][1000 genomes]
rs28644493	0.84[EUR][1000 genomes]
rs4502653	0.83[EUR][1000 genomes]
rs488440	0.84[TSI][hapmap]
rs58813617	0.96[EUR][1000 genomes]
rs62312545	0.81[EUR][1000 genomes]
rs6446983	0.82[EUR][1000 genomes]
rs6446984	0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs6446985	0.85[EUR][1000 genomes]
rs6814880	0.82[ASW][hapmap];0.83[CEU][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6819605	0.97[TSI][hapmap];0.86[EUR][1000 genomes]
rs6820992	0.83[CEU][hapmap];0.90[JPT][hapmap];0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6821664	0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs6835734	0.82[ASW][hapmap];0.83[CEU][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.84[LWK][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6854723	0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs715844	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7659389	0.84[EUR][1000 genomes]
rs7663269	0.96[CEU][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs7665105	0.84[EUR][1000 genomes]
rs7670535	0.81[EUR][1000 genomes]
rs7672588	0.84[EUR][1000 genomes]
rs7680463	0.87[CEU][hapmap];0.91[EUR][1000 genomes]
rs7681912	0.89[TSI][hapmap]
rs9997322	0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs9997788	0.81[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	nsv525980	chr4:74731526-75382209	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1009099	chr4:75089233-75726206	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10010575	ANKRD56	cis	parietal	SCAN
rs10010575	CXCL3	cis	cerebellum	SCAN
rs10010575	RCHY1	cis	parietal	SCAN
rs10010575	CNOT6L	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:75186000-75192000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr4:75187000-75192800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr4:75187600-75192400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr4:75187600-75192600	Weak transcription	NHEK	skin
5	chr4:75187600-75192800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr4:75187600-75192800	Weak transcription	HMEC	breast
7	chr4:75188000-75190400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr4:75189000-75190400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr4:75189200-75190400	Flanking Active TSS	K562	blood
10	chr4:75189200-75190600	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr4:75189200-75190600	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr4:75189600-75190800	Enhancers	Primary hematopoietic stem cells	blood
13	chr4:75190200-75190600	Enhancers	A549	lung

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