Variant report

Variant	rs4889068
Chromosome Location	chr16:80060221-80060222
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:80059154..80062850-chr16:80065920..80069891,5	MCF-7	breast:
2	chr16:80058380..80061170-chr16:80073042..80075693,3	MCF-7	breast:
3	chr16:80052898..80058811-chr16:80059069..80065197,11	MCF-7	breast:
4	chr16:79640662..79643059-chr16:80057931..80060430,2	MCF-7	breast:
5	chr16:80058579..80060805-chr16:80116598..80118912,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260237	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1115722	0.84[EUR][1000 genomes]
rs11639802	0.81[JPT][hapmap]
rs11640960	0.82[JPT][hapmap]
rs11645922	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12716881	0.93[EUR][1000 genomes]
rs12921255	0.99[EUR][1000 genomes]
rs13333795	0.98[EUR][1000 genomes]
rs1478505	0.89[EUR][1000 genomes]
rs1478506	0.89[EUR][1000 genomes]
rs2199645	0.83[EUR][1000 genomes]
rs34941385	0.83[EUR][1000 genomes]
rs4354957	0.86[CEU][hapmap];0.89[EUR][1000 genomes]
rs4363873	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs4365299	0.91[CEU][hapmap];0.93[GIH][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes]
rs4402582	0.99[EUR][1000 genomes]
rs4407073	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs4500741	0.95[CEU][hapmap];0.97[EUR][1000 genomes]
rs4500745	0.88[EUR][1000 genomes]
rs4545830	0.84[EUR][1000 genomes]
rs4888067	0.95[EUR][1000 genomes]
rs4889067	1.00[CEU][hapmap];0.96[GIH][hapmap];0.81[MEX][hapmap];0.92[TSI][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4889084	0.91[EUR][1000 genomes]
rs4889086	0.86[CEU][hapmap];0.91[EUR][1000 genomes]
rs4889090	0.90[CEU][hapmap];0.91[EUR][1000 genomes]
rs4889092	0.88[EUR][1000 genomes]
rs4889093	0.83[EUR][1000 genomes]
rs6564727	0.89[EUR][1000 genomes]
rs6564728	0.82[CEU][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes]
rs6564729	0.88[EUR][1000 genomes]
rs6564730	0.88[EUR][1000 genomes]
rs7184607	0.88[EUR][1000 genomes]
rs7185080	0.84[EUR][1000 genomes]
rs7192544	0.86[CEU][hapmap];0.91[EUR][1000 genomes]
rs7192753	0.82[CEU][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes]
rs7193465	0.87[CEU][hapmap];0.96[GIH][hapmap];0.84[TSI][hapmap];0.93[EUR][1000 genomes]
rs8050142	0.86[CEU][hapmap];0.94[TSI][hapmap];0.92[EUR][1000 genomes]
rs8050160	0.86[CEU][hapmap];0.92[EUR][1000 genomes]
rs8050173	0.84[EUR][1000 genomes]
rs8057937	0.83[EUR][1000 genomes]
rs8059251	0.91[EUR][1000 genomes]
rs9937844	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.96[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9940390	0.84[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	nsv573285	chr16:79158182-80127326	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv573294	chr16:80005642-80131944	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4889068	RFWD3	cis	parietal	SCAN
rs4889068	MATR3	trans	cerebellum	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:80058000-80060600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr16:80058000-80060600	Weak transcription	HSMM	muscle
3	chr16:80058000-80061000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr16:80058000-80061000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr16:80058000-80061000	Weak transcription	Placenta	Placenta
6	chr16:80058000-80061000	Weak transcription	Small Intestine	intestine
7	chr16:80058000-80061200	Weak transcription	Right Atrium	heart
8	chr16:80058000-80062200	Weak transcription	Esophagus	oesophagus
9	chr16:80058200-80060400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr16:80058200-80060400	Weak transcription	HMEC	breast
11	chr16:80058200-80060600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr16:80058200-80060800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr16:80058200-80060800	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr16:80058200-80060800	Weak transcription	K562	blood
15	chr16:80058200-80060800	Weak transcription	NH-A	brain
16	chr16:80058400-80060800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr16:80058400-80060800	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr16:80058400-80061000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr16:80058400-80061000	Weak transcription	Osteobl	bone
20	chr16:80058600-80060600	Weak transcription	HUVEC	blood vessel
21	chr16:80058800-80060800	Enhancers	A549	lung
22	chr16:80059000-80060800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr16:80059400-80060400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr16:80059600-80060600	Weak transcription	Duodenum Mucosa	Duodenum
25	chr16:80059600-80060800	Weak transcription	Fetal Stomach	stomach
26	chr16:80059600-80060800	Weak transcription	Stomach Smooth Muscle	stomach
27	chr16:80059600-80060800	Weak transcription	HSMMtube	muscle
28	chr16:80060200-80061200	Enhancers	NHEK	skin
29	chr16:80060200-80061400	Enhancers	ES-I3 Cell Line	embryonic stem cell

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