Variant report

Variant	rs1579780
Chromosome Location	chr2:55916154-55916155
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55915025..55917034-chr2:55917366..55919436,2	MCF-7	breast:
2	chr2:55904255..55906446-chr2:55915981..55918234,2	K562	blood:
3	chr2:55915324..55917701-chr2:55918761..55921401,5	K562	blood:
4	chr2:55915939..55918877-chr2:55919426..55922860,4	MCF-7	breast:
5	chr2:55908913..55911082-chr2:55915955..55917919,2	K562	blood:

Variant related genes	Relation type
ENSG00000138035	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10496043	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10496047	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12470253	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12471135	0.82[AMR][1000 genomes]
rs12472098	0.82[AMR][1000 genomes]
rs12476169	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17278148	1.00[ASN][1000 genomes]
rs17278197	1.00[ASN][1000 genomes]
rs17369240	1.00[ASN][1000 genomes]
rs17737937	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17738659	0.94[AMR][1000 genomes]
rs17792798	0.82[AMR][1000 genomes]
rs17792822	0.82[AMR][1000 genomes]
rs17800851	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41281507	0.82[AMR][1000 genomes]
rs4640430	0.93[EUR][1000 genomes]
rs4671247	0.82[AMR][1000 genomes]
rs4671251	1.00[ASN][1000 genomes]
rs4671256	1.00[ASN][1000 genomes]
rs4672053	0.82[AMR][1000 genomes]
rs4672057	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4672059	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4672060	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4672062	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4672064	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55635545	1.00[ASN][1000 genomes]
rs55919620	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56071955	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56286204	1.00[ASN][1000 genomes]
rs56299972	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs56769899	1.00[ASN][1000 genomes]
rs6729021	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6741902	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72812189	1.00[ASN][1000 genomes]
rs72812199	1.00[ASN][1000 genomes]
rs72814203	1.00[ASN][1000 genomes]
rs72814204	1.00[ASN][1000 genomes]
rs72814206	1.00[ASN][1000 genomes]
rs72814216	1.00[ASN][1000 genomes]
rs72814217	1.00[ASN][1000 genomes]
rs72814219	1.00[ASN][1000 genomes]
rs72814230	1.00[ASN][1000 genomes]
rs72814233	1.00[ASN][1000 genomes]
rs72814235	1.00[ASN][1000 genomes]
rs72814236	1.00[ASN][1000 genomes]
rs72814242	1.00[ASN][1000 genomes]
rs73940304	1.00[ASN][1000 genomes]
rs7568378	1.00[ASN][1000 genomes]
rs7569732	1.00[ASN][1000 genomes]
rs7584017	1.00[ASN][1000 genomes]
rs7586423	1.00[ASN][1000 genomes]
rs7603050	1.00[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	nsv531374	chr2:55653723-56299784	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv834080	chr2:55741036-55927928	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	esv2757798	chr2:55747239-55981074	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	esv2759050	chr2:55747239-55981074	Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv1008452	chr2:55809191-55987274	Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	esv2762645	chr2:55892248-55963418	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	esv2760573	chr2:55903016-55941440	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv9802	chr2:55910254-55939253	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	esv16137	chr2:55910848-55938746	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv442740	chr2:55914790-55938579	Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv514069	chr2:55914952-55938116	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55846800-55919800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:55858200-55920400	Weak transcription	Fetal Heart	heart
3	chr2:55864400-55919600	Weak transcription	NHLF	lung
4	chr2:55866600-55920000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr2:55870400-55920000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr2:55870600-55920000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr2:55870800-55920400	Weak transcription	Aorta	Aorta
8	chr2:55871000-55920000	Weak transcription	Spleen	Spleen
9	chr2:55873200-55919800	Weak transcription	Small Intestine	intestine
10	chr2:55874800-55920200	Weak transcription	Pancreas	Pancrea
11	chr2:55879000-55917600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr2:55883000-55919800	Weak transcription	HSMMtube	muscle
13	chr2:55889800-55918400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr2:55892400-55919800	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr2:55892600-55917000	Strong transcription	Dnd41	blood
16	chr2:55894000-55919800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr2:55895800-55920000	Weak transcription	Right Ventricle	heart
18	chr2:55904200-55916400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr2:55904200-55920600	Weak transcription	Stomach Mucosa	stomach
20	chr2:55904600-55920200	Weak transcription	Gastric	stomach
21	chr2:55907400-55920000	Weak transcription	Fetal Kidney	kidney
22	chr2:55907600-55919800	Weak transcription	NHDF-Ad	bronchial
23	chr2:55907800-55919800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr2:55908600-55919800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr2:55909200-55920200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr2:55910000-55919800	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr2:55910000-55920000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr2:55910000-55920000	Weak transcription	Esophagus	oesophagus
29	chr2:55910200-55919800	Weak transcription	Thymus	Thymus
30	chr2:55910400-55919800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr2:55910400-55920200	Weak transcription	Left Ventricle	heart
32	chr2:55910600-55919800	Weak transcription	Colonic Mucosa	Colon
33	chr2:55910600-55919800	Weak transcription	Fetal Brain Male	brain
34	chr2:55910600-55920000	Weak transcription	Lung	lung
35	chr2:55910600-55920200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr2:55910800-55916400	Strong transcription	A549	lung
37	chr2:55911200-55918000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr2:55911400-55916400	Weak transcription	K562	blood
39	chr2:55911600-55920000	Weak transcription	Fetal Stomach	stomach
40	chr2:55912000-55919600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr2:55912000-55920400	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr2:55912600-55919800	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr2:55912600-55919800	Weak transcription	Brain Germinal Matrix	brain
44	chr2:55912600-55919800	Weak transcription	Fetal Brain Female	brain
45	chr2:55912600-55920400	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr2:55912800-55919600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr2:55912800-55919800	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr2:55912800-55920000	Weak transcription	Brain Angular Gyrus	brain
49	chr2:55913000-55919600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr2:55913200-55919800	Weak transcription	Stomach Smooth Muscle	stomach

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