Variant report

Variant	rs11882588
Chromosome Location	chr19:39420194-39420195
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr19:39419973-39422967	A549	lung:	n/a	chr19:39421022-39421040 chr19:39421023-39421039
2	CTCF	chr19:39420176-39422260	SK-N-SH	brain:	n/a	chr19:39421022-39421040 chr19:39421023-39421039
3	POLR2A	chr19:39418846-39427915	PANC-1	pancreas:	n/a	n/a
4	FOSL2	chr19:39420127-39422594	A549	lung:	n/a	chr19:39421460-39421469
5	RAD21	chr19:39420156-39422195	SK-N-SH	brain:	n/a	chr19:39421923-39421933 chr19:39421087-39421101
6	ELF1	chr19:39420120-39420461	K562	blood:	n/a	n/a
7	POLR2A	chr19:39419835-39427960	PANC-1	pancreas:	n/a	n/a
8	POLR2A	chr19:39420189-39422075	H1-hESC	embryonic stem cell:	n/a	n/a
9	BCL3	chr19:39420121-39422645	A549	lung:	n/a	chr19:39421086-39421099 chr19:39421078-39421091

No data

(count:19 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39336974..39342883-chr19:39419267..39423173,13	K562	blood:
2	chr19:39398838..39403067-chr19:39419638..39422578,4	MCF-7	breast:
3	chr19:39338595..39344864-chr19:39418604..39422934,11	K562	blood:
4	chr19:39360175..39362471-chr19:39419567..39421419,2	MCF-7	breast:
5	chr19:39322407..39324148-chr19:39419876..39421918,2	K562	blood:
6	chr19:39226181..39228990-chr19:39419347..39420876,2	K562	blood:
7	chr19:39386472..39392494-chr19:39418718..39424791,9	K562	blood:
8	chr19:39326367..39329872-chr19:39419342..39422625,3	MCF-7	breast:
9	chr19:39388885..39392214-chr19:39419332..39422757,5	MCF-7	breast:
10	chr19:39358835..39360669-chr19:39419879..39421985,2	K562	blood:
11	chr19:39411897..39413585-chr19:39419804..39422534,2	K562	blood:
12	chr19:39401097..39402936-chr19:39418975..39421481,2	K562	blood:
13	chr19:39338960..39343184-chr19:39419440..39422855,6	MCF-7	breast:
14	chr19:39338909..39344654-chr19:39419169..39426961,19	MCF-7	breast:
15	chr19:39414900..39416436-chr19:39417401..39420305,2	K562	blood:
16	chr19:39226859..39228990-chr19:39419347..39420977,2	K562	blood:
17	chr19:39406282..39408716-chr19:39419182..39421050,3	K562	blood:
18	chr19:39411214..39414705-chr19:39419221..39421908,4	MCF-7	breast:
19	chr19:39370268..39372714-chr19:39419858..39422598,3	K562	blood:

No data

Variant related genes	Relation type
MRPS12	TF binding region
ENSG00000269050	Chromatin interaction
ENSG00000104823	Chromatin interaction
ENSG00000104824	Chromatin interaction
ENSG00000068903	Chromatin interaction
ENSG00000104835	Chromatin interaction
ENSG00000182472	Chromatin interaction
ENSG00000262484	Chromatin interaction
ENSG00000267892	Chromatin interaction
ENSG00000187994	Chromatin interaction
ENSG00000104825	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10407879	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10410176	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10412886	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10415194	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1134180	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12460327	0.90[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12462170	0.84[ASN][1000 genomes]
rs2116854	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2116855	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28375245	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs751941	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	esv1837023	chr19:39190588-39425722	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39391200-39420800	Weak transcription	Small Intestine	intestine
2	chr19:39391600-39420600	Weak transcription	Right Atrium	heart
3	chr19:39398000-39420600	Weak transcription	Psoas Muscle	Psoas
4	chr19:39402800-39420200	Weak transcription	Colon Smooth Muscle	Colon
5	chr19:39403600-39420400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr19:39403800-39420200	Weak transcription	Fetal Brain Male	brain
7	chr19:39406800-39420200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr19:39409200-39420400	Weak transcription	Stomach Mucosa	stomach
9	chr19:39411600-39420400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr19:39411600-39420400	Weak transcription	Fetal Heart	heart
11	chr19:39412800-39420600	Weak transcription	Rectal Smooth Muscle	rectum
12	chr19:39413200-39420200	Weak transcription	Primary B cells from cord blood	blood
13	chr19:39413200-39420200	Weak transcription	NH-A	brain
14	chr19:39413200-39420200	Weak transcription	NHLF	lung
15	chr19:39413200-39420400	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr19:39413200-39420400	Weak transcription	Fetal Kidney	kidney
17	chr19:39413200-39420800	Weak transcription	Aorta	Aorta
18	chr19:39415400-39420200	Weak transcription	NHDF-Ad	bronchial
19	chr19:39415600-39420200	Weak transcription	Brain Angular Gyrus	brain
20	chr19:39415600-39420400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr19:39415600-39420400	Weak transcription	Colonic Mucosa	Colon
22	chr19:39415600-39420600	Weak transcription	Pancreas	Pancrea
23	chr19:39415800-39420200	Weak transcription	Primary T cells from cord blood	blood
24	chr19:39415800-39420200	Weak transcription	HUVEC	blood vessel
25	chr19:39415800-39420400	Weak transcription	HSMM	muscle
26	chr19:39416200-39420200	Weak transcription	Brain Substantia Nigra	brain
27	chr19:39416200-39420200	Weak transcription	Osteobl	bone
28	chr19:39416400-39420200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr19:39416400-39420200	Weak transcription	Brain Hippocampus Middle	brain
30	chr19:39416400-39420200	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr19:39416400-39420200	Weak transcription	HMEC	breast
32	chr19:39416400-39420400	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr19:39416400-39420400	Weak transcription	HSMMtube	muscle
34	chr19:39416400-39420600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr19:39416400-39420600	Enhancers	Primary T cells fromperipheralblood	blood
36	chr19:39416400-39420600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr19:39416600-39420200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr19:39416800-39420400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr19:39417000-39420200	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr19:39417000-39420200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr19:39417000-39420200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr19:39417000-39420200	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr19:39417000-39420200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr19:39417000-39420200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr19:39417000-39420200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr19:39417000-39420200	Weak transcription	Brain Anterior Caudate	brain
47	chr19:39417000-39420200	Weak transcription	Brain Cingulate Gyrus	brain
48	chr19:39417000-39420200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr19:39417000-39420200	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr19:39417000-39420200	Weak transcription	Stomach Smooth Muscle	stomach

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