Variant report

Variant	rs12462908
Chromosome Location	chr19:52633013-52633014
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	chr19:52632666..52634991-chr19:52642095..52643875,2	K562	blood:
2	chr19:52631135..52633164-chr19:52639000..52640822,2	K562	blood:

Variant related genes	Relation type
ENSG00000204611	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10405763	0.86[ASN][1000 genomes]
rs10405987	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10415918	0.91[ASN][1000 genomes]
rs10423034	0.90[ASN][1000 genomes]
rs11084145	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12162225	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12462872	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12609137	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12610551	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16983496	0.90[ASN][1000 genomes]
rs17779542	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17835808	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs45468391	0.91[ASN][1000 genomes]
rs59541557	0.82[ASN][1000 genomes]
rs67861844	0.82[ASN][1000 genomes]
rs8100114	0.91[ASN][1000 genomes]
rs8105609	0.91[ASN][1000 genomes]
rs8108125	0.90[ASN][1000 genomes]
rs8112502	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065410	chr19:52103914-52889530	Genic enhancers Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	596 gene(s)	inside rSNPs	diseases
2	esv3366000	chr19:52491073-52842946	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv1066015	chr19:52502213-52890308	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv544059	chr19:52502213-52890308	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	esv3433050	chr19:52595705-52639973	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv960859	chr19:52631598-52633888	ZNF genes & repeats Weak transcription Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52606800-52640200	ZNF genes & repeats	Liver	Liver
2	chr19:52607000-52634000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr19:52609800-52639000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr19:52609800-52640200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
5	chr19:52613600-52639000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr19:52615200-52640200	ZNF genes & repeats	Fetal Brain Female	brain
7	chr19:52615600-52640200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr19:52616200-52634200	ZNF genes & repeats	Primary T cells from cord blood	blood
9	chr19:52616200-52640000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr19:52616200-52641200	ZNF genes & repeats	Dnd41	blood
11	chr19:52616200-52641400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr19:52616200-52641600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr19:52616400-52641400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr19:52616800-52634000	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
15	chr19:52617000-52640200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
16	chr19:52617200-52634000	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
17	chr19:52617200-52640200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr19:52617400-52634200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr19:52617400-52641400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
20	chr19:52617800-52635600	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
21	chr19:52618000-52640200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr19:52618400-52635000	ZNF genes & repeats	Fetal Intestine Large	intestine
23	chr19:52618600-52633600	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
24	chr19:52620800-52634000	Strong transcription	Placenta Amnion	Placenta Amnion
25	chr19:52624200-52634400	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
26	chr19:52624200-52640200	ZNF genes & repeats	Fetal Intestine Small	intestine
27	chr19:52625000-52634200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr19:52625400-52635800	ZNF genes & repeats	Lung	lung
29	chr19:52626600-52634800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
30	chr19:52626600-52640400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr19:52627200-52640200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr19:52628800-52639800	ZNF genes & repeats	Fetal Stomach	stomach
33	chr19:52628800-52641400	Weak transcription	Brain Substantia Nigra	brain
34	chr19:52629000-52641200	Weak transcription	Right Ventricle	heart
35	chr19:52629200-52633200	Weak transcription	Hela-S3	cervix
36	chr19:52629200-52640800	Weak transcription	Rectal Smooth Muscle	rectum
37	chr19:52629400-52633200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr19:52629400-52641200	Weak transcription	Colon Smooth Muscle	Colon
39	chr19:52629400-52641600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr19:52629600-52633200	Weak transcription	Brain Cingulate Gyrus	brain
41	chr19:52629600-52641800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr19:52629800-52633800	Strong transcription	Skeletal Muscle Female	skeletal muscle
43	chr19:52629800-52634200	Strong transcription	Left Ventricle	heart
44	chr19:52629800-52641200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr19:52630000-52633400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr19:52630200-52633600	Strong transcription	Muscle Satellite Cultured Cells	--
47	chr19:52630200-52633800	Strong transcription	Brain Angular Gyrus	brain
48	chr19:52630200-52633800	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr19:52630400-52633200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr19:52630600-52634200	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell

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