Variant report

Variant	rs248939
Chromosome Location	chr19:19883549-19883550
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:19869687..19871477-chr19:19882175..19885147,2	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10407920	0.84[EUR][1000 genomes]
rs10419635	0.81[CEU][hapmap];0.80[EUR][1000 genomes]
rs11878280	0.83[EUR][1000 genomes]
rs12973032	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs12975121	0.84[EUR][1000 genomes]
rs2304171	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs23654	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs248938	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs248940	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs248941	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs248955	0.88[EUR][1000 genomes]
rs2878398	0.84[EUR][1000 genomes]
rs34277739	0.85[EUR][1000 genomes]
rs35018071	0.84[EUR][1000 genomes]
rs35280091	0.85[EUR][1000 genomes]
rs4808989	0.82[CEU][hapmap]
rs4990741	0.84[EUR][1000 genomes]
rs60041535	0.83[EUR][1000 genomes]
rs7246983	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs7252985	0.83[CEU][hapmap];0.85[EUR][1000 genomes]
rs8111421	0.82[CEU][hapmap]
rs919785	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1828240	chr19:19591146-19900900	Weak transcription Enhancers Genic enhancers Flanking Active TSS 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	55 gene(s)	inside rSNPs	diseases
2	nsv1063273	chr19:19591146-20061367	ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv911312	chr19:19861682-19917662	Strong transcription ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv458375	chr19:19863014-19949209	Weak transcription Active TSS Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv578798	chr19:19863014-19949209	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv911313	chr19:19866371-19936078	Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv911314	chr19:19866371-20021046	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv519535	chr19:19871250-20595412	Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
9	nsv911315	chr19:19872093-20021046	Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs248939	ZNF506	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19862800-19886400	Weak transcription	Pancreas	Pancrea
2	chr19:19865200-19886400	Weak transcription	Right Ventricle	heart
3	chr19:19866200-19886000	Weak transcription	Brain Hippocampus Middle	brain
4	chr19:19869400-19886400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr19:19870400-19885400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr19:19879400-19886200	Weak transcription	Brain Substantia Nigra	brain
7	chr19:19881200-19886400	Weak transcription	Stomach Smooth Muscle	stomach
8	chr19:19881400-19886400	Weak transcription	NH-A	brain
9	chr19:19882600-19885400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr19:19883400-19886400	Weak transcription	NHDF-Ad	bronchial

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