Variant report

Variant	rs597995
Chromosome Location	chr19:39573008-39573009
allele	C/G
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	RCOR1	chr19:39572948-39573100	K562	blood:	n/a	n/a
2	POLR2A	chr19:39572561-39575566	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:39572549..39576644-chr19:39655893..39659798,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC011443.1-1	chr19:39572421-39575494	expReg_chr19_5096_+

Variant related genes	Relation type
ENSG00000183760	TF binding region
ENSG00000130669	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10407957	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10408661	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12151180	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2569365	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34738600	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs377373	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs380679	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs384605	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs385681	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs392005	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs392135	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs393559	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs395387	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs396616	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs397189	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs400011	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs420682	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs426076	0.95[CEU][hapmap];1.00[CHB][hapmap];0.80[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs452666	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs453853	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4802015	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4803196	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4803197	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs482679	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs487456	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs578940	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs602744	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs609327	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs620642	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs621580	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs648192	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs648635	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs665998	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs690812	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs691059	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs691114	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs691256	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs691266	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs691391	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs691890	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs692294	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs692343	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs692347	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs774727	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs774927	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs774928	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv458571	chr19:39533754-39628050	Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv579508	chr19:39533754-39628050	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv522530	chr19:39552150-39573918	Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1067028	chr19:39567228-39622846	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv1060469	chr19:39567228-39624790	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	nsv833829	chr19:39569681-39730777	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
7	nsv432048	chr19:39572060-39850060	Bivalent/Poised TSS Bivalent Enhancer Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39565400-39573200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr19:39567400-39574000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr19:39569800-39573400	Weak transcription	Brain Substantia Nigra	brain
4	chr19:39569800-39573400	Weak transcription	Hela-S3	cervix
5	chr19:39569800-39573600	Weak transcription	HUVEC	blood vessel
6	chr19:39569800-39573800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr19:39569800-39573800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr19:39570000-39573200	Weak transcription	NHEK	skin
9	chr19:39570200-39573200	Weak transcription	Brain Anterior Caudate	brain
10	chr19:39570400-39573600	Weak transcription	Osteobl	bone
11	chr19:39570600-39573200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr19:39571400-39573400	Weak transcription	A549	lung
13	chr19:39572200-39573800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr19:39573000-39573200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr19:39573000-39573200	Bivalent Enhancer	Brain Inferior Temporal Lobe	brain
16	chr19:39573000-39573200	Bivalent Enhancer	Fetal Intestine Large	intestine
17	chr19:39573000-39573400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr19:39573000-39573400	Bivalent Enhancer	Brain Cingulate Gyrus	brain
19	chr19:39573000-39573600	Enhancers	NHDF-Ad	bronchial
20	chr19:39573000-39573800	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr19:39573000-39573800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr19:39573000-39574000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr19:39573000-39574200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr19:39573000-39575600	Flanking Active TSS	HMEC	breast

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