Variant report

Variant	rs12419479
Chromosome Location	chr11:59033612-59033613
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	chr11:59032632..59035314-chr11:59038415..59042026,3	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11600401	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11606140	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11607278	0.88[CEU][hapmap];0.88[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11607673	0.85[EUR][1000 genomes]
rs17582175	0.91[CHD][hapmap]
rs2000478	0.88[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2211912	0.85[CEU][hapmap];0.85[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs34697089	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3944255	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4369428	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4939269	0.92[CEU][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs5029315	0.85[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs610123	0.88[CEU][hapmap];0.84[JPT][hapmap]
rs61903328	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6591509	0.88[CEU][hapmap];0.89[CHB][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7113633	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7113936	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7131079	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7928981	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7942710	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7944135	0.88[CEU][hapmap];0.82[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.81[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7944319	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7952377	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050013	chr11:58394598-59221090	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv948365	chr11:58515163-59156405	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	esv1821250	chr11:58925860-59059179	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	esv3351601	chr11:58979308-59052763	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	esv3381199	chr11:59015574-59068938	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12419479	DTX4	cis	Esophagus Muscularis	GTEx
rs12419479	SNORD28	cis	cerebellum	SCAN
rs12419479	UBE2L6	cis	parietal	SCAN
rs12419479	OR5B2	cis	parietal	SCAN
rs12419479	OR5B21	cis	cerebellum	SCAN
rs12419479	MS4A12	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:59028200-59034000	Weak transcription	GM12878-XiMat	blood
2	chr11:59029800-59039000	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr11:59029800-59040400	Enhancers	Primary B cells from cord blood	blood
4	chr11:59030000-59035400	Enhancers	Primary B cells from peripheral blood	blood
5	chr11:59031200-59035400	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr11:59031400-59039000	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr11:59031600-59033800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr11:59031600-59035000	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr11:59031800-59036800	Enhancers	Placenta	Placenta
10	chr11:59032000-59036200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr11:59032200-59034400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr11:59032200-59036000	Enhancers	HMEC	breast
13	chr11:59032200-59036200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr11:59032400-59036000	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr11:59032600-59039200	Weak transcription	Spleen	Spleen
16	chr11:59033400-59036000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr11:59033600-59034600	Weak transcription	Liver	Liver

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