Variant report

Variant	rs28850368
Chromosome Location	chr4:120554313-120554314
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:120552728..120554364-chr4:120974086..120975727,2	MCF-7	breast:

Extended variants
information (count: 54 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs10009566	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10012252	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10022185	0.88[ASN][1000 genomes]
rs10050092	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11098534	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12499377	0.84[EUR][1000 genomes]
rs12504773	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12505735	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12512646	0.83[EUR][1000 genomes]
rs12642411	0.88[ASN][1000 genomes]
rs13101722	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13122709	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13136462	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17051352	0.87[ASN][1000 genomes]
rs2389874	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2389879	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2389880	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2389882	0.88[ASN][1000 genomes]
rs2389885	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2389886	0.88[ASN][1000 genomes]
rs2389887	0.88[ASN][1000 genomes]
rs28394116	0.82[EUR][1000 genomes]
rs28535956	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28578366	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28787668	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34278750	0.88[ASN][1000 genomes]
rs34835603	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3756156	0.82[EUR][1000 genomes]
rs3806808	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4504231	0.84[EUR][1000 genomes]
rs4833624	0.82[EUR][1000 genomes]
rs58583086	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59867181	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6534149	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6832740	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6855918	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7664440	0.88[ASN][1000 genomes]
rs7671096	0.87[ASN][1000 genomes]
rs7676296	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7680914	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7693919	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7695292	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916641	chr4:119780023-120777320	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv532739	chr4:120392824-121098103	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv1010753	chr4:120429028-120684310	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv537233	chr4:120429028-120684310	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1006572	chr4:120432494-120694243	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	esv3466099	chr4:120552743-120556240	Enhancers Weak transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	esv3466100	chr4:120552768-120556201	Enhancers Weak transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	esv3466098	chr4:120552770-120556212	Weak transcription Enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	esv3466102	chr4:120552788-120556162	Enhancers Weak transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	esv3466101	chr4:120552835-120556137	Weak transcription Enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	esv17708	chr4:120552839-120556129	Weak transcription Enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	esv3466103	chr4:120552849-120556136	Weak transcription Enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs28850368	LOC645513	Cis_1M	lymphoblastoid	RTeQTL
rs28850368	RP11-33B1.1	cis	lung	GTEx
rs28850368	RP11-33B1.1	cis	Whole Blood	GTEx
rs28850368	RP11-33B1.4	cis	Whole Blood	GTEx
rs28850368	FLJ14186///LOC284701///LOC441124///LOC728624	Cis_1M	lymphoblastoid	RTeQTL
rs28850368	RP11-33B1.1	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120550600-120554400	Weak transcription	Pancreas	Pancrea
2	chr4:120552400-120558600	Weak transcription	Fetal Stomach	stomach
3	chr4:120554000-120559400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr4:120554000-120559400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr4:120554000-120559400	Weak transcription	NHLF	lung
6	chr4:120554200-120554600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr4:120554200-120557400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr4:120554200-120559400	Weak transcription	Osteobl	bone

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