Variant report

Variant	rs17829765
Chromosome Location	chr4:75196731-75196732
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr4:75193547..75202304-chr4:75225099..75233434,18	K562	blood:
2	chr4:75195874..75197815-chr4:75217759..75219523,2	K562	blood:
3	chr4:75193835..75196818-chr4:75546936..75549420,2	K562	blood:
4	chr4:75161899..75164379-chr4:75195063..75196891,2	K562	blood:
5	chr4:75196361..75198336-chr4:75221116..75223874,2	K562	blood:
6	chr4:75196510..75198336-chr4:75220610..75222616,2	K562	blood:
7	chr4:75192372..75204703-chr4:75227413..75239566,26	K562	blood:
8	chr4:75195893..75197465-chr4:75242238..75243930,2	K562	blood:
9	chr4:75195012..75198024-chr4:75202040..75205774,3	K562	blood:
10	chr4:75196204..75197946-chr4:75212119..75215441,3	K562	blood:
11	chr4:75196224..75197946-chr4:75213014..75215441,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000124882	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10010575	0.87[CEU][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes]
rs10013212	0.83[EUR][1000 genomes]
rs10017409	0.89[TSI][hapmap]
rs10018373	0.93[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.81[EUR][1000 genomes]
rs10019396	0.84[EUR][1000 genomes]
rs10023519	0.82[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs10026687	0.82[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs1037824	0.81[EUR][1000 genomes]
rs10938112	0.84[EUR][1000 genomes]
rs11737662	0.80[TSI][hapmap]
rs11942725	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1246575	0.80[TSI][hapmap]
rs1246578	0.80[TSI][hapmap]
rs1246591	0.80[TSI][hapmap]
rs1246594	1.00[JPT][hapmap]
rs1265327	0.80[TSI][hapmap]
rs1460016	0.80[TSI][hapmap]
rs16850883	0.80[CEU][hapmap];0.81[EUR][1000 genomes]
rs16850941	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17232394	0.87[EUR][1000 genomes]
rs2045616	0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs2045617	0.81[EUR][1000 genomes]
rs2061508	0.89[TSI][hapmap]
rs28378517	0.86[EUR][1000 genomes]
rs28436705	0.82[EUR][1000 genomes]
rs4502653	0.87[EUR][1000 genomes]
rs488440	0.80[TSI][hapmap]
rs58813617	0.89[EUR][1000 genomes]
rs62312545	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6446984	0.89[TSI][hapmap]
rs6814880	0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs6819605	0.89[TSI][hapmap]
rs6820992	0.81[EUR][1000 genomes]
rs6821664	0.82[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs6835734	0.89[TSI][hapmap];0.80[EUR][1000 genomes]
rs6854723	0.89[ASW][hapmap];0.82[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.82[MEX][hapmap];0.98[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs715844	0.90[EUR][1000 genomes]
rs7663269	0.83[CEU][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes]
rs7670535	0.86[EUR][1000 genomes]
rs7680463	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7681912	0.80[TSI][hapmap]
rs9684145	0.85[MKK][hapmap]
rs9997322	0.89[ASW][hapmap];0.82[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.82[MEX][hapmap];0.98[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9997788	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	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17829765	CXCL3	cis	cerebellum	SCAN
rs17829765	ANKRD56	cis	parietal	SCAN
rs17829765	CNOT6L	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:75193200-75196800	Active TSS	K562	blood
2	chr4:75194600-75209400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr4:75195000-75209600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr4:75196200-75208000	Weak transcription	NHEK	skin
5	chr4:75196400-75196800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr4:75196400-75197200	Enhancers	Primary hematopoietic stem cells	blood
7	chr4:75196400-75197400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr4:75196400-75197400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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