Variant report

Variant	rs2450439
Chromosome Location	chr19:56646367-56646368
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:56644274..56647215-chr19:56650542..56653019,3	MCF-7	breast:
2	chr19:56642703..56647128-chr19:56651543..56655262,4	MCF-7	breast:
3	chr19:56637204..56640116-chr19:56644041..56647745,4	K562	blood:
4	chr19:56632432..56634662-chr19:56644261..56647544,4	MCF-7	breast:
5	chr19:56645494..56648781-chr19:56650139..56653742,5	K562	blood:
6	chr19:56635952..56638231-chr19:56646331..56649019,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000167685	Chromatin interaction
ENSG00000142409	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs11673628	0.80[ASN][1000 genomes]
rs12459102	0.82[ASN][1000 genomes]
rs12981138	0.87[ASN][1000 genomes]
rs12983086	0.85[ASN][1000 genomes]
rs2631625	0.94[ASN][1000 genomes]
rs2631627	0.99[ASN][1000 genomes]
rs2631628	0.99[ASN][1000 genomes]
rs2631631	0.98[ASN][1000 genomes]
rs2631637	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2631640	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2637088	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2637092	0.99[ASN][1000 genomes]
rs2637094	0.96[ASN][1000 genomes]
rs2637097	0.97[ASN][1000 genomes]
rs2637114	0.97[ASN][1000 genomes]
rs2932757	0.97[ASN][1000 genomes]
rs473953	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs478402	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4801676	0.82[ASN][1000 genomes]
rs481936	0.81[ASN][1000 genomes]
rs490345	0.99[ASN][1000 genomes]
rs492078	0.82[ASN][1000 genomes]
rs497453	0.93[ASN][1000 genomes]
rs501798	0.81[ASN][1000 genomes]
rs504350	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs506547	0.96[ASN][1000 genomes]
rs509897	0.84[ASN][1000 genomes]
rs517021	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs517582	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs522980	0.86[ASN][1000 genomes]
rs524778	0.91[ASN][1000 genomes]
rs524829	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs524988	0.93[ASN][1000 genomes]
rs525827	0.96[ASN][1000 genomes]
rs527715	0.96[ASN][1000 genomes]
rs533640	0.81[ASN][1000 genomes]
rs533734	0.81[ASN][1000 genomes]
rs535393	0.82[ASN][1000 genomes]
rs536342	0.81[ASN][1000 genomes]
rs537425	0.82[ASN][1000 genomes]
rs544365	0.92[ASN][1000 genomes]
rs545570	0.87[ASN][1000 genomes]
rs547002	0.90[ASN][1000 genomes]
rs547945	0.89[ASN][1000 genomes]
rs564050	0.81[ASN][1000 genomes]
rs564973	0.86[ASN][1000 genomes]
rs565879	0.85[ASN][1000 genomes]
rs569310	0.91[ASN][1000 genomes]
rs572851	0.96[ASN][1000 genomes]
rs578990	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs578991	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs583330	0.96[ASN][1000 genomes]
rs587702	0.89[ASN][1000 genomes]
rs588574	0.81[ASN][1000 genomes]
rs592827	0.94[ASN][1000 genomes]
rs599405	0.88[ASN][1000 genomes]
rs619934	0.81[ASN][1000 genomes]
rs626821	0.96[ASN][1000 genomes]
rs628090	0.87[ASN][1000 genomes]
rs629544	0.94[ASN][1000 genomes]
rs640654	0.96[ASN][1000 genomes]
rs643133	0.96[ASN][1000 genomes]
rs643174	0.94[ASN][1000 genomes]
rs659424	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs662308	0.99[ASN][1000 genomes]
rs662763	0.97[ASN][1000 genomes]
rs665082	0.99[ASN][1000 genomes]
rs665846	0.82[ASN][1000 genomes]
rs665857	0.99[ASN][1000 genomes]
rs667438	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs667523	0.91[ASN][1000 genomes]
rs667974	0.91[ASN][1000 genomes]
rs669866	0.90[ASN][1000 genomes]
rs677127	0.99[ASN][1000 genomes]
rs677142	0.81[ASN][1000 genomes]
rs678540	0.99[ASN][1000 genomes]
rs684653	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs685117	0.87[ASN][1000 genomes]
rs8103672	0.84[ASN][1000 genomes]
rs8108818	0.84[ASN][1000 genomes]
rs9676765	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	nsv517365	chr19:56592286-56674548	Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
9	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
10	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
11	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
12	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:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56637800-56647600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:56638600-56651200	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr19:56638800-56651800	Weak transcription	Spleen	Spleen
4	chr19:56639000-56647600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr19:56640800-56649000	Enhancers	Primary neutrophils fromperipheralblood	blood
6	chr19:56642600-56647800	Enhancers	Placenta	Placenta
7	chr19:56644000-56651200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr19:56644000-56651200	Weak transcription	Lung	lung
9	chr19:56644000-56651200	Weak transcription	Rectal Smooth Muscle	rectum
10	chr19:56644200-56646800	Weak transcription	Liver	Liver
11	chr19:56644200-56647600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr19:56644200-56647600	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr19:56644200-56647600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr19:56644200-56647600	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr19:56644200-56647600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr19:56644200-56649400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr19:56644200-56651200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr19:56644200-56651200	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr19:56644200-56651200	Weak transcription	Brain Anterior Caudate	brain
20	chr19:56644200-56651200	Weak transcription	Fetal Kidney	kidney
21	chr19:56644200-56651400	Weak transcription	Right Atrium	heart
22	chr19:56644400-56651200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr19:56644800-56649000	Weak transcription	Adipose Nuclei	Adipose
24	chr19:56645000-56647600	Weak transcription	Stomach Smooth Muscle	stomach
25	chr19:56645000-56651200	Weak transcription	Aorta	Aorta
26	chr19:56645200-56646800	Enhancers	NHEK	skin
27	chr19:56645200-56647600	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr19:56645400-56647000	Enhancers	Sigmoid Colon	Sigmoid Colon
29	chr19:56645400-56651200	Weak transcription	NH-A	brain
30	chr19:56645400-56651800	Enhancers	Pancreas	Pancrea
31	chr19:56645600-56646800	Enhancers	HMEC	breast
32	chr19:56645600-56647200	Enhancers	Rectal Mucosa Donor 31	rectum
33	chr19:56645600-56647600	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr19:56645800-56646600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr19:56645800-56646800	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr19:56645800-56647000	Weak transcription	HepG2	liver
37	chr19:56645800-56647600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr19:56645800-56647800	Weak transcription	Colonic Mucosa	Colon
39	chr19:56645800-56648800	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr19:56645800-56648800	Weak transcription	A549	lung
41	chr19:56645800-56649000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr19:56645800-56651200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr19:56645800-56651200	Weak transcription	Fetal Muscle Trunk	muscle
44	chr19:56645800-56651200	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr19:56645800-56651200	Weak transcription	HSMM	muscle
46	chr19:56645800-56651400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr19:56645800-56651600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr19:56646000-56646400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr19:56646000-56646400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr19:56646000-56647600	Weak transcription	K562	blood

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