Variant report

Variant	rs4257894
Chromosome Location	chr6:110498209-110498210
allele	A/C
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	chr6:110498149-110498386	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:110496307..110499261-chr6:110709602..110711774,2	MCF-7	breast:

Variant related genes	Relation type
CDC40	TF binding region

Extended variants
information (count: 71 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs11153226	1.00[ASW][hapmap];0.94[CEU][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11751590	0.84[ASW][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11757055	0.84[ASW][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.86[TSI][hapmap];0.90[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12110744	1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12660119	0.89[ASN][1000 genomes]
rs12660791	0.84[ASW][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12662013	0.93[ASN][1000 genomes]
rs12665849	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12665858	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1462490	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1462492	1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1462493	0.94[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2002630	0.91[ASN][1000 genomes]
rs4299857	1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4339500	0.84[ASW][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.86[TSI][hapmap];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4509164	1.00[ASW][hapmap];0.94[CEU][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4945850	1.00[ASW][hapmap];0.94[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4945851	0.88[CEU][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4947048	0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4947051	0.84[ASW][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4947058	0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.95[ASN][1000 genomes]
rs56122480	0.96[ASN][1000 genomes]
rs56135788	0.95[ASN][1000 genomes]
rs56287427	0.98[ASN][1000 genomes]
rs57983455	0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs60495849	0.94[ASN][1000 genomes]
rs61020234	0.91[ASN][1000 genomes]
rs6568633	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6568634	1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.86[TSI][hapmap]
rs6913554	1.00[CHD][hapmap];0.82[GIH][hapmap];0.93[MEX][hapmap];0.99[ASN][1000 genomes]
rs6915379	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6918148	0.93[CHD][hapmap];0.85[GIH][hapmap];0.92[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6925392	0.92[ASN][1000 genomes]
rs6926540	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6927667	0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6927697	1.00[ASW][hapmap];0.94[CEU][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];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6927722	0.84[ASW][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap];0.94[ASN][1000 genomes]
rs6928684	0.88[ASN][1000 genomes]
rs6938106	0.94[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6938139	0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.95[ASN][1000 genomes]
rs6938653	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs719849	0.95[ASN][1000 genomes]
rs73533834	0.82[ASN][1000 genomes]
rs73535810	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs73535817	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs73535821	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs73535837	0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs73535838	0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs73537927	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73537938	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73537949	0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7744828	1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7766850	0.87[ASN][1000 genomes]
rs9372247	0.87[EUR][1000 genomes]
rs9372248	0.80[ASN][1000 genomes]
rs9374156	0.82[ASN][1000 genomes]
rs9400359	0.82[ASN][1000 genomes]
rs9400360	0.82[ASN][1000 genomes]
rs9481045	0.82[ASN][1000 genomes]
rs9481047	0.81[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9481048	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9487317	0.87[ASN][1000 genomes]
rs9487318	0.81[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9487319	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9487321	1.00[JPT][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv886535	chr6:110377006-110551463	Strong transcription Genic enhancers Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	esv2757188	chr6:110389926-110504680	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	esv2759462	chr6:110389926-110504680	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	esv1792799	chr6:110411065-110566597	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv886536	chr6:110426046-110502831	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv948824	chr6:110443685-110889332	Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4257894	WASF1	cis	Artery Tibial	GTEx
rs4257894	WASF1	cis	Muscle Skeletal	GTEx
rs4257894	WASF1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:110449200-110498600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:110462600-110498800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr6:110470200-110499400	Weak transcription	Primary hematopoietic stem cells	blood
4	chr6:110471600-110499600	Weak transcription	Primary B cells from cord blood	blood
5	chr6:110490400-110498800	Weak transcription	Brain Germinal Matrix	brain
6	chr6:110492800-110499400	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr6:110495400-110500000	Weak transcription	Gastric	stomach
8	chr6:110495600-110498600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr6:110495800-110498600	Weak transcription	HepG2	liver
10	chr6:110495800-110498800	Weak transcription	Stomach Smooth Muscle	stomach
11	chr6:110496000-110498600	Weak transcription	Brain Anterior Caudate	brain
12	chr6:110496000-110498600	Weak transcription	Brain Hippocampus Middle	brain
13	chr6:110496000-110498800	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr6:110496000-110499600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr6:110496200-110498800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr6:110496400-110498800	Weak transcription	Fetal Brain Male	brain
17	chr6:110496600-110498600	Active TSS	Fetal Brain Female	brain
18	chr6:110496600-110498800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr6:110496800-110498400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr6:110496800-110498600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr6:110496800-110498800	Weak transcription	Brain Cingulate Gyrus	brain
22	chr6:110496800-110498800	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr6:110496800-110499800	Weak transcription	Ovary	ovary
24	chr6:110497000-110498800	Weak transcription	Hela-S3	cervix
25	chr6:110497000-110499200	Weak transcription	Brain Substantia Nigra	brain
26	chr6:110497000-110499400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr6:110497800-110499200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr6:110498000-110502200	Active TSS	Brain Angular Gyrus	brain

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