Variant report

Variant	rs2561562
Chromosome Location	chr19:41150086-41150087
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:41120433..41122395-chr19:41149709..41152254,3	MCF-7	breast:
2	chr19:41120316..41124225-chr19:41147891..41152450,4	K562	blood:
3	chr19:41145219..41147338-chr19:41149537..41152318,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000090006	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10409296	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10411059	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10411347	0.95[ASN][1000 genomes]
rs10421223	0.92[ASN][1000 genomes]
rs2561555	0.94[ASN][1000 genomes]
rs2604860	0.93[ASN][1000 genomes]
rs2604861	0.97[ASN][1000 genomes]
rs2604904	0.94[ASN][1000 genomes]
rs2604907	0.94[ASN][1000 genomes]
rs4278858	0.90[ASN][1000 genomes]
rs67971171	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7258709	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1830682	chr19:40880127-41270055	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	139 gene(s)	inside rSNPs	diseases
2	nsv911714	chr19:41006426-41165252	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer 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	33 gene(s)	inside rSNPs	diseases
3	nsv1057634	chr19:41019512-41174259	Enhancers Active TSS Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv911720	chr19:41033109-41156940	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
5	nsv911722	chr19:41040334-41176403	Bivalent Enhancer Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv911723	chr19:41075990-41195279	Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	nsv1064699	chr19:41086506-41174259	Genic enhancers Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv911724	chr19:41089505-41165252	Bivalent/Poised TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
9	nsv911727	chr19:41111069-41200511	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
10	nsv911728	chr19:41111069-41211056	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
11	nsv870022	chr19:41113071-41178982	Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	27 gene(s)	inside rSNPs	diseases
12	esv1800615	chr19:41127465-41270055	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
13	nsv2489	chr19:41145034-41182170	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases
14	nsv1058707	chr19:41146147-41200820	Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41140800-41152600	Weak transcription	Right Atrium	heart
2	chr19:41145400-41153000	Enhancers	Fetal Stomach	stomach
3	chr19:41146600-41150800	Weak transcription	Colon Smooth Muscle	Colon
4	chr19:41146800-41151000	Weak transcription	NHDF-Ad	bronchial
5	chr19:41146800-41151200	Weak transcription	Stomach Smooth Muscle	stomach
6	chr19:41146800-41152400	Weak transcription	Colonic Mucosa	Colon
7	chr19:41146800-41152400	Weak transcription	Lung	lung
8	chr19:41146800-41157000	Weak transcription	Spleen	Spleen
9	chr19:41147000-41151000	Weak transcription	Left Ventricle	heart
10	chr19:41147000-41151200	Weak transcription	Placenta	Placenta
11	chr19:41147000-41151600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr19:41147000-41151600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr19:41147000-41151600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr19:41147000-41151800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr19:41147000-41151800	Weak transcription	Fetal Heart	heart
16	chr19:41147200-41151800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr19:41147400-41151200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr19:41147400-41151200	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr19:41147400-41151600	Weak transcription	HSMMtube	muscle
20	chr19:41147400-41151800	Weak transcription	NH-A	brain
21	chr19:41147400-41152000	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr19:41147600-41150600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr19:41147600-41151400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr19:41147600-41151400	Weak transcription	HUVEC	blood vessel
25	chr19:41147600-41151600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr19:41147600-41151600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr19:41147600-41151600	Weak transcription	Osteobl	bone
28	chr19:41147600-41151800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr19:41147600-41152400	Weak transcription	Ovary	ovary
30	chr19:41147600-41152400	Weak transcription	NHLF	lung
31	chr19:41148000-41151200	Weak transcription	Fetal Muscle Leg	muscle
32	chr19:41148200-41151000	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr19:41149000-41151000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr19:41149000-41151000	Weak transcription	Fetal Muscle Trunk	muscle
35	chr19:41149200-41150800	Weak transcription	Adipose Nuclei	Adipose
36	chr19:41149400-41151600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr19:41149800-41150800	Weak transcription	A549	lung
38	chr19:41149800-41151400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr19:41149800-41152000	Weak transcription	Fetal Lung	lung
40	chr19:41150000-41151800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links