Variant report

Variant	rs266125
Chromosome Location	chr19:51296796-51296797
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:51295777..51298371-chr5:133339070..133341774,2	MCF-7	breast:
2	chr19:51293560..51298277-chr19:51413419..51418761,7	K562	blood:
3	chr19:51296429..51299323-chr19:51371370..51374659,5	K562	blood:
4	chr19:51296075..51301998-chr19:51356744..51362542,6	K562	blood:
5	chr19:51207455..51209701-chr19:51296263..51298998,3	K562	blood:
6	chr19:51287157..51292690-chr19:51292694..51297699,7	MCF-7	breast:
7	chr19:51226381..51234126-chr19:51290973..51302468,19	K562	blood:
8	chr19:51295821..51300740-chr19:51378160..51386074,8	K562	blood:
9	chr19:51295380..51297114-chr19:51411572..51413706,2	K562	blood:
10	chr19:51295821..51300740-chr19:51378160..51386074,7	K562	blood:
11	chr19:51191963..51194196-chr19:51295538..51298347,2	K562	blood:
12	chr19:51206207..51210755-chr19:51296263..51301273,7	K562	blood:
13	chr19:51226381..51234126-chr19:51290973..51298243,11	K562	blood:
14	chr19:51225708..51229784-chr19:51294422..51298363,4	MCF-7	breast:
15	chr1:51984448..51984999-chr19:51296761..51297730,2	Hela-S3	cervix:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C19orf48-2	chr19:51296689-51296841	ENSG00000268375.1

No data

Variant related genes	Relation type
ENSG00000271737	Chromatin interaction
ENSG00000261341	Chromatin interaction
ENSG00000213585	Chromatin interaction
ENSG00000167749	Chromatin interaction
ENSG00000105472	Chromatin interaction
ENSG00000161681	Chromatin interaction
ENSG00000167751	Chromatin interaction
ENSG00000085832	Chromatin interaction
ENSG00000142515	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10425724	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1054713	0.85[ASN][1000 genomes]
rs11672844	0.97[ASN][1000 genomes]
rs197589	0.90[ASN][1000 genomes]
rs1978605	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2247289	0.97[ASN][1000 genomes]
rs2411334	0.89[ASN][1000 genomes]
rs2434449	0.97[ASN][1000 genomes]
rs2456584	0.97[ASN][1000 genomes]
rs2456585	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2560931	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2560933	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2659058	0.82[ASN][1000 genomes]
rs2659059	0.97[ASN][1000 genomes]
rs2659099	0.90[ASN][1000 genomes]
rs2659100	0.89[ASN][1000 genomes]
rs2659101	0.86[ASN][1000 genomes]
rs2659103	0.83[ASN][1000 genomes]
rs2659104	0.83[ASN][1000 genomes]
rs266116	0.90[ASN][1000 genomes]
rs266122	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs266123	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs266127	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs266128	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5516	0.86[ASN][1000 genomes]
rs56164547	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59524380	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs788886	0.93[ASN][1000 genomes]
rs788887	0.94[ASN][1000 genomes]
rs788889	0.97[ASN][1000 genomes]
rs788890	0.97[ASN][1000 genomes]
rs788891	0.97[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	nsv1060760	chr19:50883425-51463712	ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
2	nsv1058177	chr19:50984774-51463712	Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
3	nsv912288	chr19:51283791-51334355	Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases
4	nsv912289	chr19:51283791-51335943	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases
5	nsv912290	chr19:51283791-51344483	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs266125	C19orf48	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:51286800-51296800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr19:51287000-51298400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr19:51287000-51298400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr19:51287200-51301200	Weak transcription	Primary B cells from cord blood	blood
5	chr19:51287400-51300000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr19:51289800-51298600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr19:51290000-51298800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr19:51291800-51303400	Weak transcription	Fetal Kidney	kidney
9	chr19:51292600-51297200	Weak transcription	Right Atrium	heart
10	chr19:51293200-51297800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr19:51293400-51300000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr19:51295600-51301000	Weak transcription	HepG2	liver
13	chr19:51295800-51299200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr19:51296000-51299000	Weak transcription	Dnd41	blood
15	chr19:51296000-51300200	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr19:51296000-51300400	Weak transcription	Fetal Lung	lung
17	chr19:51296200-51296800	Weak transcription	Fetal Intestine Small	intestine
18	chr19:51296200-51298600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr19:51296400-51297400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr19:51296400-51298200	Weak transcription	Brain Germinal Matrix	brain
21	chr19:51296400-51298400	Weak transcription	Brain Cingulate Gyrus	brain
22	chr19:51296400-51300600	Weak transcription	Brain Angular Gyrus	brain
23	chr19:51296600-51298600	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr19:51296600-51298600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr19:51296600-51304200	Weak transcription	HSMM	muscle

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