Variant report

Variant	rs2560889
Chromosome Location	chr19:52857105-52857106
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11084149	0.85[ASN][1000 genomes]
rs1120185	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2247986	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2251476	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2263900	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2560879	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2560884	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2560886	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2560887	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2560888	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2560972	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2560977	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2560978	1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2560981	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2560986	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2657936	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
3	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
4	nsv833873	chr19:52788939-52937281	Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv1066537	chr19:52794424-53044977	Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
6	nsv544060	chr19:52794424-53044977	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv458742	chr19:52808986-52866171	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
8	nsv580008	chr19:52808986-52866171	ZNF genes & repeats Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
9	esv3401193	chr19:52818960-52909749	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
10	nsv912300	chr19:52832830-52928039	Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv912301	chr19:52835210-52914233	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52840400-52857400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr19:52840400-52865400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr19:52840600-52858800	Weak transcription	Rectal Smooth Muscle	rectum
4	chr19:52840600-52861200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr19:52847200-52860000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr19:52848000-52862600	Weak transcription	Fetal Heart	heart
7	chr19:52848400-52870400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr19:52848800-52858400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr19:52849600-52861400	ZNF genes & repeats	Fetal Intestine Small	intestine
10	chr19:52849800-52872200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr19:52850400-52862000	Strong transcription	Fetal Brain Female	brain
12	chr19:52850800-52860600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr19:52850800-52861200	Strong transcription	Stomach Smooth Muscle	stomach
14	chr19:52850800-52870200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
15	chr19:52850800-52870200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr19:52851000-52857200	Strong transcription	Duodenum Smooth Muscle	Duodenum
17	chr19:52851200-52859000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr19:52851600-52864200	Strong transcription	Brain Germinal Matrix	brain
19	chr19:52852000-52858200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr19:52852200-52858000	Weak transcription	Fetal Kidney	kidney
21	chr19:52852400-52858400	Weak transcription	Colonic Mucosa	Colon
22	chr19:52852400-52858800	Weak transcription	Fetal Brain Male	brain
23	chr19:52852600-52857200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr19:52852600-52857200	Weak transcription	Osteobl	bone
25	chr19:52853400-52857200	Weak transcription	HSMMtube	muscle
26	chr19:52853400-52858400	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr19:52853600-52858200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr19:52854000-52857400	Weak transcription	Brain Substantia Nigra	brain
29	chr19:52854200-52860400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr19:52854600-52861200	Strong transcription	Fetal Muscle Leg	muscle
31	chr19:52854800-52859400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
32	chr19:52855200-52859000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr19:52855200-52860600	Strong transcription	Fetal Stomach	stomach
34	chr19:52855400-52858200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr19:52855400-52859800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr19:52855800-52857200	Weak transcription	Brain Angular Gyrus	brain
37	chr19:52855800-52857400	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
38	chr19:52855800-52860400	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
39	chr19:52856000-52858200	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr19:52856000-52858400	Weak transcription	Pancreas	Pancrea
41	chr19:52856000-52858400	Weak transcription	Psoas Muscle	Psoas
42	chr19:52856000-52859600	Weak transcription	NHDF-Ad	bronchial
43	chr19:52856400-52857800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr19:52856400-52861400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr19:52856600-52857600	Genic enhancers	Brain Hippocampus Middle	brain
46	chr19:52856600-52858200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr19:52856600-52859200	Strong transcription	Dnd41	blood
48	chr19:52856600-52859600	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
49	chr19:52856600-52860600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr19:52856600-52864200	ZNF genes & repeats	Liver	Liver

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