Variant report

Variant	rs2615588
Chromosome Location	chr19:53039532-53039533
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	chr19:53039240..53039740-chr19:53289638..53290383,2	NB4	blood:
2	chr19:53029459..53032258-chr19:53036873..53039549,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000189190	Chromatin interaction
ENSG00000198482	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs11667348	0.83[EUR][1000 genomes]
rs11668903	0.86[EUR][1000 genomes]
rs12610240	0.85[EUR][1000 genomes]
rs1676153	0.94[ASN][1000 genomes]
rs2045754	0.83[ASN][1000 genomes]
rs2608513	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2608522	0.92[ASN][1000 genomes]
rs2608527	0.93[ASN][1000 genomes]
rs2615586	0.93[ASN][1000 genomes]
rs2615587	0.95[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2617795	0.94[ASN][1000 genomes]
rs2633502	0.94[ASN][1000 genomes]
rs2633513	0.97[ASN][1000 genomes]
rs2633514	0.91[ASN][1000 genomes]
rs2633517	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2868688	0.84[EUR][1000 genomes]
rs2925976	0.98[ASN][1000 genomes]
rs326439	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs326440	0.90[ASN][1000 genomes]
rs326441	0.89[ASN][1000 genomes]
rs326442	0.83[ASN][1000 genomes]
rs326443	0.91[ASN][1000 genomes]
rs326444	0.95[ASN][1000 genomes]
rs326446	0.93[ASN][1000 genomes]
rs326447	0.90[ASN][1000 genomes]
rs326448	0.90[ASN][1000 genomes]
rs326449	0.90[ASN][1000 genomes]
rs368922	0.94[ASN][1000 genomes]
rs375267	0.94[ASN][1000 genomes]
rs376595	0.92[ASN][1000 genomes]
rs396663	0.91[ASN][1000 genomes]
rs400709	0.91[ASN][1000 genomes]
rs402737	0.97[ASN][1000 genomes]
rs410046	0.90[ASN][1000 genomes]
rs413751	0.88[ASN][1000 genomes]
rs413814	0.93[ASN][1000 genomes]
rs417599	0.92[ASN][1000 genomes]
rs422195	0.91[ASN][1000 genomes]
rs429367	0.89[ASN][1000 genomes]
rs434709	0.91[ASN][1000 genomes]
rs434788	0.97[ASN][1000 genomes]
rs439618	0.91[ASN][1000 genomes]
rs440545	0.89[ASN][1000 genomes]
rs441549	0.94[ASN][1000 genomes]
rs441850	0.90[ASN][1000 genomes]
rs445500	0.90[ASN][1000 genomes]
rs449671	0.91[ASN][1000 genomes]
rs4802966	0.83[EUR][1000 genomes]
rs4802967	0.83[EUR][1000 genomes]
rs4802971	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4802972	0.92[ASN][1000 genomes]
rs520958	0.90[ASN][1000 genomes]
rs521703	0.94[ASN][1000 genomes]
rs529698	0.97[ASN][1000 genomes]
rs532449	0.97[ASN][1000 genomes]
rs606521	0.93[ASN][1000 genomes]
rs606538	0.92[ASN][1000 genomes]
rs606914	0.97[ASN][1000 genomes]
rs607477	0.96[ASN][1000 genomes]
rs62117197	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62117198	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62117199	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62119356	0.87[EUR][1000 genomes]
rs62119359	0.90[ASN][1000 genomes]
rs642493	0.86[ASN][1000 genomes]
rs653483	0.90[ASN][1000 genomes]
rs656541	0.99[ASN][1000 genomes]
rs666356	0.88[ASN][1000 genomes]
rs668882	0.98[ASN][1000 genomes]
rs685200	0.97[ASN][1000 genomes]
rs688646	0.90[ASN][1000 genomes]
rs781129	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs92520	0.93[ASN][1000 genomes]
rs9676916	0.86[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066537	chr19:52794424-53044977	Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv544060	chr19:52794424-53044977	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv580026	chr19:52937100-53059872	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1063648	chr19:52938131-53041119	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1057296	chr19:52950339-53396986	Weak transcription Active TSS ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv978841	chr19:52983057-53088237	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv1066717	chr19:52993620-53041995	Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1064342	chr19:52996710-53041119	ZNF genes & repeats Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv1055859	chr19:53001299-53041119	Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1060656	chr19:53001299-53041995	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv510772	chr19:53037211-53103470	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53032200-53057000	Weak transcription	Hela-S3	cervix
2	chr19:53032600-53049800	Weak transcription	HepG2	liver
3	chr19:53033800-53040200	ZNF genes & repeats	Liver	Liver
4	chr19:53036400-53040000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr19:53036400-53040400	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
6	chr19:53037400-53040400	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
7	chr19:53037600-53051800	Weak transcription	K562	blood
8	chr19:53038000-53040800	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr19:53038200-53039800	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr19:53038200-53040000	Active TSS	Fetal Brain Female	brain
11	chr19:53038200-53040200	Active TSS	iPS-15b Cell Line	embryonic stem cell
12	chr19:53038200-53040200	Active TSS	GM12878-XiMat	blood
13	chr19:53038200-53040400	Active TSS	HUES64 Cell Line	embryonic stem cell
14	chr19:53038400-53039600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr19:53038400-53039600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr19:53038400-53039600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr19:53038400-53040000	Active TSS	H1 Cell Line	embryonic stem cell
18	chr19:53038400-53040000	Active TSS	iPS-18 Cell Line	embryonic stem cell
19	chr19:53038400-53040000	Active TSS	Brain Inferior Temporal Lobe	brain
20	chr19:53038400-53040200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
21	chr19:53038400-53040200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr19:53038400-53040400	Active TSS	H9 Cell Line	embryonic stem cell
23	chr19:53038400-53040400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr19:53038400-53040400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr19:53038400-53040400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr19:53038600-53039800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr19:53038600-53039800	Active TSS	Primary T helper naive cells from peripheral blood	blood
28	chr19:53038600-53039800	Active TSS	Primary T helper cells PMA-I stimulated	--
29	chr19:53038600-53039800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr19:53038600-53039800	Active TSS	Aorta	Aorta
31	chr19:53038600-53039800	Active TSS	Fetal Intestine Small	intestine
32	chr19:53038600-53039800	Active TSS	Fetal Thymus	thymus
33	chr19:53038600-53039800	Active TSS	Psoas Muscle	Psoas
34	chr19:53038600-53039800	Active TSS	Thymus	Thymus
35	chr19:53038600-53040000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr19:53038600-53040000	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr19:53038600-53040000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
38	chr19:53038600-53040000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr19:53038600-53040000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr19:53038600-53040000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
41	chr19:53038600-53040000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr19:53038600-53040000	Active TSS	Brain Angular Gyrus	brain
43	chr19:53038600-53040000	Active TSS	Brain Cingulate Gyrus	brain
44	chr19:53038600-53040000	Active TSS	Brain Hippocampus Middle	brain
45	chr19:53038600-53040000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr19:53038600-53040000	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 29	rectum
47	chr19:53038600-53040000	Active TSS	HSMM	muscle
48	chr19:53038600-53040000	Active TSS	NH-A	brain
49	chr19:53038600-53040200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr19:53038600-53040200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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