Variant report

Variant	rs274144
Chromosome Location	chr19:56675974-56675975
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	chr19:56670800..56672784-chr19:56675448..56678240,2	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs2631642	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2631652	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs274141	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs274145	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs274146	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs274151	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs274154	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs274155	0.85[ASN][1000 genomes]
rs274156	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs274159	0.89[EUR][1000 genomes]
rs274163	0.89[EUR][1000 genomes]
rs274165	0.89[EUR][1000 genomes]
rs274167	0.87[EUR][1000 genomes]
rs274180	0.90[EUR][1000 genomes]
rs274182	0.90[EUR][1000 genomes]
rs3103059	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3103060	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs480528	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs481291	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs482506	0.97[ASN][1000 genomes]
rs487922	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs488118	0.97[ASN][1000 genomes]
rs488196	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs565171	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs581486	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61283021	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs650832	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs651800	0.97[ASN][1000 genomes]
rs652204	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs671061	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs672956	0.89[ASN][1000 genomes]
rs679082	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs901476	0.90[EUR][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	nsv1056598	chr19:56331762-56703428	Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
2	nsv1064371	chr19:56418215-56842450	ZNF genes & repeats Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
3	nsv1057316	chr19:56418215-56849458	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
4	nsv580354	chr19:56505685-56723492	Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
5	nsv523651	chr19:56537528-56707048	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
6	nsv1057820	chr19:56555942-56720262	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
7	nsv528998	chr19:56578238-56707048	Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
8	nsv912513	chr19:56592286-56685463	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
9	nsv521744	chr19:56592286-56686953	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
10	nsv912516	chr19:56601298-56981382	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	93 gene(s)	inside rSNPs	diseases
11	nsv528361	chr19:56638845-56688570	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56654000-56681600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr19:56661400-56676200	Weak transcription	Fetal Brain Male	brain
3	chr19:56670200-56678000	Weak transcription	HepG2	liver
4	chr19:56670800-56681600	Weak transcription	A549	lung
5	chr19:56670800-56681800	Weak transcription	NHEK	skin
6	chr19:56671600-56683200	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr19:56671800-56676000	Weak transcription	Small Intestine	intestine
8	chr19:56672000-56677000	Weak transcription	Colonic Mucosa	Colon
9	chr19:56672200-56683200	Weak transcription	Rectal Smooth Muscle	rectum
10	chr19:56672400-56683200	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr19:56672600-56676800	Weak transcription	Brain Angular Gyrus	brain
12	chr19:56672600-56678800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr19:56672600-56681200	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr19:56672600-56681800	Weak transcription	Ovary	ovary
15	chr19:56672600-56684200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr19:56672600-56685600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr19:56672800-56676600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr19:56672800-56681200	Weak transcription	Duodenum Mucosa	Duodenum
19	chr19:56672800-56681600	Weak transcription	Esophagus	oesophagus
20	chr19:56672800-56683200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr19:56672800-56683200	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr19:56672800-56683400	Weak transcription	Fetal Intestine Large	intestine
23	chr19:56673000-56676000	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr19:56673000-56676200	Enhancers	Primary hematopoietic stem cells	blood
25	chr19:56673000-56676200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr19:56673000-56690000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr19:56673200-56676200	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr19:56673200-56676200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr19:56673200-56676400	Weak transcription	Brain Hippocampus Middle	brain
30	chr19:56673200-56676600	Weak transcription	Lung	lung
31	chr19:56673200-56678200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr19:56673200-56678200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr19:56673200-56681800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr19:56673200-56681800	Weak transcription	Adipose Nuclei	Adipose
35	chr19:56673200-56683200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr19:56673200-56683200	Weak transcription	Fetal Muscle Leg	muscle
37	chr19:56673400-56676000	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr19:56673400-56676200	Weak transcription	Primary T cells from cord blood	blood
39	chr19:56673400-56676200	Enhancers	Dnd41	blood
40	chr19:56673400-56676400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr19:56673400-56676400	Weak transcription	Brain Anterior Caudate	brain
42	chr19:56673400-56681600	Weak transcription	Pancreas	Pancrea
43	chr19:56673400-56683200	Weak transcription	Liver	Liver
44	chr19:56673600-56683200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr19:56673800-56676000	Weak transcription	Fetal Intestine Small	intestine
46	chr19:56673800-56681600	Weak transcription	Spleen	Spleen
47	chr19:56673800-56683200	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr19:56674000-56676000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr19:56674000-56676200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr19:56674000-56676600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links