Variant report

Variant	rs2089275
Chromosome Location	chr19:52775301-52775302
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:52764752..52766794-chr19:52774661..52777312,2	K562	blood:
2	chr19:52772026..52776261-chr19:52781637..52786393,5	K562	blood:
3	chr19:52772381..52778282-chr19:52778346..52783668,9	MCF-7	breast:
4	chr19:52692994..52696358-chr19:52773094..52775949,3	MCF-7	breast:
5	chr19:52774375..52777116-chr19:52786827..52789950,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000208002	Chromatin interaction
ENSG00000105568	Chromatin interaction
ENSG00000196214	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10404635	0.90[ASN][1000 genomes]
rs10425462	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10425644	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2560871	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2560873	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2560875	0.81[AFR][1000 genomes]
rs2560877	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2657923	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2657924	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2657926	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2657928	0.81[AFR][1000 genomes]
rs2657930	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28718737	0.81[ASN][1000 genomes]
rs56211703	0.96[ASN][1000 genomes]
rs56369375	0.90[ASN][1000 genomes]
rs62110397	1.00[ASN][1000 genomes]
rs62110398	1.00[ASN][1000 genomes]
rs7255504	0.90[ASN][1000 genomes]
rs8107325	1.00[ASN][1000 genomes]
rs8113537	0.90[ASN][1000 genomes]
rs9304726	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52774000-52775600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr19:52774000-52776000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr19:52774000-52776000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr19:52774000-52776000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr19:52774000-52776000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr19:52774000-52776600	Weak transcription	Esophagus	oesophagus
7	chr19:52774000-52776800	Weak transcription	Psoas Muscle	Psoas
8	chr19:52774000-52780000	Weak transcription	Aorta	Aorta
9	chr19:52774000-52780200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr19:52774000-52786600	Weak transcription	Right Ventricle	heart
11	chr19:52774000-52787200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr19:52774200-52775600	Weak transcription	NH-A	brain
13	chr19:52774200-52776000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr19:52774200-52776000	Weak transcription	NHEK	skin
15	chr19:52774200-52777400	Weak transcription	HSMMtube	muscle
16	chr19:52774200-52786600	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr19:52774200-52797400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr19:52774200-52799600	Weak transcription	Hela-S3	cervix
19	chr19:52774400-52775400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr19:52774400-52775600	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr19:52774400-52775600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
22	chr19:52774400-52775600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr19:52774400-52775600	Enhancers	Duodenum Smooth Muscle	Duodenum
24	chr19:52774400-52775800	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr19:52774400-52775800	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr19:52774400-52776000	Strong transcription	HSMM	muscle
27	chr19:52774400-52777000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr19:52774400-52777200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr19:52774400-52777200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr19:52774400-52777600	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr19:52774400-52777800	ZNF genes & repeats	A549	lung
32	chr19:52774400-52778400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr19:52774400-52778400	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
34	chr19:52774400-52779200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr19:52774400-52781000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr19:52774400-52782000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr19:52774400-52786600	Weak transcription	Osteobl	bone
38	chr19:52774400-52787000	Weak transcription	HUVEC	blood vessel
39	chr19:52774400-52787400	Weak transcription	NHDF-Ad	bronchial
40	chr19:52774600-52775400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr19:52774600-52775400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr19:52774600-52775400	Weak transcription	Stomach Smooth Muscle	stomach
43	chr19:52774600-52775600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr19:52774600-52775600	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
45	chr19:52774600-52775600	Weak transcription	Fetal Intestine Large	intestine
46	chr19:52774600-52775600	Strong transcription	NHLF	lung
47	chr19:52774600-52776000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr19:52774600-52776200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr19:52774600-52776600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr19:52774600-52777000	Weak transcription	Stomach Mucosa	stomach

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