Variant report

Variant	rs59045002
Chromosome Location	chr19:18956699-18956700
allele	A/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	CTCF	chr19:18956660-18956810	GM12868	blood:	n/a	n/a
2	POLR2A	chr19:18955976-18956983	GM12892	blood:	n/a	n/a
3	POLR2A	chr19:18955665-18957549	GM12878	blood:	n/a	n/a
4	POLR2A	chr19:18956574-18956882	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:18954859..18958448-chr19:18959389..18963601,5	MCF-7	breast:
2	chr19:18900192..18902235-chr19:18954832..18957574,2	K562	blood:
3	chr19:18954190..18955830-chr19:18956609..18958808,3	MCF-7	breast:

Variant related genes	Relation type
UPF1	TF binding region
ENSG00000005007	Chromatin interaction
ENSG00000105664	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs2238653	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2238654	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2238655	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2238656	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2238657	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4808861	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4808863	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs757115	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][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	nsv911293	chr19:18872917-19050957	Flanking Active TSS Genic enhancers Strong transcription Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv911294	chr19:18872917-19093619	Active TSS Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv833777	chr19:18875936-19031076	Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv911297	chr19:18928480-19077385	Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	nsv911298	chr19:18928480-19093619	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	nsv911299	chr19:18939954-18984843	Active TSS Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv911300	chr19:18944025-19093619	Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18946200-18958200	Weak transcription	Fetal Kidney	kidney
2	chr19:18947200-18958400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr19:18948600-18957200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr19:18948800-18957800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr19:18948800-18958400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr19:18948800-18959000	Weak transcription	Primary hematopoietic stem cells	blood
7	chr19:18949200-18956800	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr19:18949200-18958400	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr19:18949800-18956800	Enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr19:18949800-18958400	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr19:18950000-18957800	Weak transcription	Primary B cells from cord blood	blood
12	chr19:18950600-18957800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr19:18950800-18956800	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr19:18950800-18956800	Enhancers	Adipose Nuclei	Adipose
15	chr19:18950800-18958600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr19:18951000-18960800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr19:18951200-18958400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr19:18951400-18957800	Weak transcription	Rectal Smooth Muscle	rectum
19	chr19:18951600-18959000	Weak transcription	Psoas Muscle	Psoas
20	chr19:18951800-18958800	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr19:18951800-18959200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr19:18951800-18977000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr19:18952000-18958000	Weak transcription	Fetal Brain Male	brain
24	chr19:18952000-18958600	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr19:18952000-18961200	Weak transcription	Small Intestine	intestine
26	chr19:18952200-18957200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr19:18952400-18956800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr19:18952400-18958600	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr19:18952600-18956800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
30	chr19:18953200-18977600	Weak transcription	Fetal Heart	heart
31	chr19:18953400-18957800	Weak transcription	Fetal Lung	lung
32	chr19:18953600-18958800	Weak transcription	Brain Germinal Matrix	brain
33	chr19:18953800-18956800	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr19:18954200-18956800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr19:18954200-18956800	Weak transcription	Brain Cingulate Gyrus	brain
36	chr19:18954200-18958400	Weak transcription	A549	lung
37	chr19:18954200-18961400	Weak transcription	Aorta	Aorta
38	chr19:18954800-18957400	Weak transcription	Brain Anterior Caudate	brain
39	chr19:18954800-18958400	Weak transcription	Hela-S3	cervix
40	chr19:18954800-18958600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr19:18954800-18979800	Strong transcription	Dnd41	blood
42	chr19:18955000-18956800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
43	chr19:18955000-18956800	Weak transcription	Fetal Intestine Large	intestine
44	chr19:18955000-18956800	Weak transcription	HepG2	liver
45	chr19:18955000-18956800	Weak transcription	HMEC	breast
46	chr19:18955000-18956800	Weak transcription	NHLF	lung
47	chr19:18955000-18957800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr19:18955000-18957800	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr19:18955000-18957800	Weak transcription	Brain Angular Gyrus	brain
50	chr19:18955000-18957800	Weak transcription	Duodenum Smooth Muscle	Duodenum

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