Variant report

Variant	rs17075335
Chromosome Location	chr3:43257188-43257189
allele	C/T
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	CTCF	chr3:43257180-43257330	GM12870	blood:	n/a	n/a
2	CTCF	chr3:43257183-43257480	H1-hESC	embryonic stem cell:	n/a	chr3:43257364-43257380

No.	Distal block	Cell Line	Cell type
1	chr3:43233608..43236021-chr3:43256055..43258322,2	MCF-7	breast:
2	chr3:43235922..43238512-chr3:43256089..43258366,2	K562	blood:
3	chr3:43256868..43257655-chr3:43265030..43265781,2	K562	blood:
4	chr3:43254448..43258211-chr3:43258239..43261327,4	K562	blood:
5	chr3:43203368..43203905-chr3:43256948..43257808,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000222331	TF binding region

Extended variants
information (count: 71 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs11129996	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11927798	0.82[EUR][1000 genomes]
rs12715387	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12715388	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13059783	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13060695	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13066699	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13074235	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13085652	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1316297	0.94[ASN][1000 genomes]
rs1320156	0.95[ASN][1000 genomes]
rs1320158	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1573931	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17075317	0.92[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.89[TSI][hapmap]
rs17075378	0.95[ASN][1000 genomes]
rs17075381	0.95[ASN][1000 genomes]
rs17075398	0.94[ASN][1000 genomes]
rs1814902	0.98[ASN][1000 genomes]
rs2372352	0.91[ASN][1000 genomes]
rs2372354	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2372355	0.95[ASN][1000 genomes]
rs2372356	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2888295	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2888296	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4016130	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4260403	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4404425	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4419357	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4444688	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4637262	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4682675	0.89[ASN][1000 genomes]
rs4682872	0.97[ASN][1000 genomes]
rs4682879	0.89[ASN][1000 genomes]
rs4683363	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4683364	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4683366	1.00[JPT][hapmap]
rs4683367	1.00[ASN][1000 genomes]
rs4683369	0.97[ASN][1000 genomes]
rs6442144	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6762503	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6781696	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6798619	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6805075	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7621298	0.85[JPT][hapmap]
rs7621511	0.95[ASN][1000 genomes]
rs7627198	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7636673	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7639584	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7639605	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7648154	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9311334	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9311335	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9311336	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9681394	0.85[JPT][hapmap]
rs9683242	0.82[JPT][hapmap]
rs9809273	0.95[ASN][1000 genomes]
rs9820946	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9822961	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9826102	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9826849	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9827911	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9833793	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9852399	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9853795	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9858012	1.00[CHB][hapmap];0.84[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9860007	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9860364	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9861337	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9861529	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9875582	0.85[CHB][hapmap];0.95[CHD][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834672	chr3:43132722-43306272	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17075335	FYCO1	cis	parietal	SCAN
rs17075335	SLC25A38	cis	parietal	SCAN
rs17075335	SNRK	cis	cerebellum	SCAN
rs17075335	PTH1R	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:43245000-43258800	Weak transcription	Right Atrium	heart
2	chr3:43247800-43259000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:43253200-43262400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr3:43253400-43259000	Weak transcription	Spleen	Spleen
5	chr3:43253600-43257400	Weak transcription	Left Ventricle	heart
6	chr3:43254000-43257200	Enhancers	HMEC	breast
7	chr3:43254000-43258000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr3:43254200-43257800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr3:43254400-43257200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr3:43256200-43266800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr3:43256200-43267000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr3:43256400-43257200	Enhancers	Stomach Mucosa	stomach
13	chr3:43256400-43257800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr3:43256400-43257800	Enhancers	Pancreas	Pancrea
15	chr3:43256600-43260600	Weak transcription	Fetal Kidney	kidney
16	chr3:43256600-43264000	Enhancers	Primary T cells from cord blood	blood
17	chr3:43256800-43261000	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr3:43256800-43264800	Enhancers	Fetal Thymus	thymus
19	chr3:43256800-43264800	Enhancers	Thymus	Thymus
20	chr3:43257000-43260400	Enhancers	NHEK	skin
21	chr3:43257000-43262400	Weak transcription	Fetal Intestine Small	intestine

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