Variant report

Variant	rs274146
Chromosome Location	chr19:56674598-56674599
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	chr19:56671026..56674616-chr19:56677144..56679269,3	K562	blood:
2	chr19:56673116..56675836-chr19:56676117..56678644,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC024580.1-1	chr19:56674226-56674872	NONHSAT068086

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs2631642	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2631652	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs274141	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs274144	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs274145	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs274151	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs274154	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs274156	0.85[EUR][1000 genomes]
rs274159	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs274163	0.87[EUR][1000 genomes]
rs274165	0.87[EUR][1000 genomes]
rs274167	0.84[EUR][1000 genomes]
rs274180	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs274182	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3103059	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3103060	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs480528	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs481291	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs482506	0.89[ASN][1000 genomes]
rs487922	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs488118	0.89[ASN][1000 genomes]
rs488196	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs565171	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs581486	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61283021	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs650832	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs651800	0.89[ASN][1000 genomes]
rs652204	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs671061	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs672956	0.81[ASN][1000 genomes]
rs679082	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs901476	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[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	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:92 , 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	chr19:56667000-56674800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr19:56668000-56675400	Weak transcription	Primary B cells from cord blood	blood
5	chr19:56668800-56674600	Weak transcription	Stomach Mucosa	stomach
6	chr19:56670200-56678000	Weak transcription	HepG2	liver
7	chr19:56670800-56675000	Weak transcription	Brain Substantia Nigra	brain
8	chr19:56670800-56675200	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr19:56670800-56675400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr19:56670800-56681600	Weak transcription	A549	lung
11	chr19:56670800-56681800	Weak transcription	NHEK	skin
12	chr19:56671000-56674600	Weak transcription	Fetal Lung	lung
13	chr19:56671000-56675400	Weak transcription	Osteobl	bone
14	chr19:56671600-56683200	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr19:56671800-56676000	Weak transcription	Small Intestine	intestine
16	chr19:56672000-56674600	Weak transcription	Aorta	Aorta
17	chr19:56672000-56677000	Weak transcription	Colonic Mucosa	Colon
18	chr19:56672200-56683200	Weak transcription	Rectal Smooth Muscle	rectum
19	chr19:56672400-56675200	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr19:56672400-56683200	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr19:56672600-56674800	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr19:56672600-56675400	Weak transcription	Primary B cells from peripheral blood	blood
23	chr19:56672600-56675600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr19:56672600-56676800	Weak transcription	Brain Angular Gyrus	brain
25	chr19:56672600-56678800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr19:56672600-56681200	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr19:56672600-56681800	Weak transcription	Ovary	ovary
28	chr19:56672600-56684200	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr19:56672600-56685600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr19:56672800-56674600	Weak transcription	Left Ventricle	heart
31	chr19:56672800-56674800	Weak transcription	NHLF	lung
32	chr19:56672800-56675000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr19:56672800-56675200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr19:56672800-56675200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr19:56672800-56675200	Weak transcription	Colon Smooth Muscle	Colon
36	chr19:56672800-56675600	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr19:56672800-56675600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr19:56672800-56676600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr19:56672800-56681200	Weak transcription	Duodenum Mucosa	Duodenum
40	chr19:56672800-56681600	Weak transcription	Esophagus	oesophagus
41	chr19:56672800-56683200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr19:56672800-56683200	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr19:56672800-56683400	Weak transcription	Fetal Intestine Large	intestine
44	chr19:56673000-56675000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr19:56673000-56675600	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr19:56673000-56676000	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr19:56673000-56676200	Enhancers	Primary hematopoietic stem cells	blood
48	chr19:56673000-56676200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr19:56673000-56690000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr19:56673200-56674800	Enhancers	K562	blood

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