Variant report

Variant	rs16859380
Chromosome Location	chr2:172272444-172272445
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:24)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:24 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:172009192..172011548-chr2:172270786..172273321,2	K562	blood:
2	chr2:172270914..172275149-chr2:172275462..172279658,6	K562	blood:
3	chr2:172015616..172017761-chr2:172271152..172272814,2	MCF-7	breast:
4	chr2:171829670..171830422-chr2:172272305..172273239,6	MCF-7	breast:
5	chr2:172271134..172274908-chr2:172289137..172291473,5	MCF-7	breast:
6	chr2:172265513..172268385-chr2:172270721..172272607,2	MCF-7	breast:
7	chr2:172269451..172273904-chr2:172275650..172277742,4	K562	blood:
8	chr2:172271657..172275800-chr2:172289994..172293745,6	K562	blood:
9	chr2:172017358..172018279-chr2:172272338..172273091,4	MCF-7	breast:
10	chr2:172020395..172022447-chr2:172272199..172274902,2	MCF-7	breast:
11	chr2:172271335..172273049-chr2:172276074..172277809,2	MCF-7	breast:
12	chr2:172267840..172270296-chr2:172270765..172273449,2	K562	blood:
13	chr2:172015744..172019134-chr2:172270782..172274226,5	K562	blood:
14	chr2:172270978..172272997-chr2:172289315..172290964,3	MCF-7	breast:
15	chr2:172016348..172019248-chr2:172270460..172274931,6	MCF-7	breast:
16	chr2:171829613..171830619-chr2:172272303..172273269,4	K562	blood:
17	chr2:171829283..171832000-chr2:172272425..172274768,3	MCF-7	breast:
18	chr2:172271841..172274486-chr2:172281833..172284953,3	K562	blood:
19	chr2:171831104..171831914-chr2:172272322..172273272,2	K562	blood:
20	chr2:172016440..172019134-chr2:172272291..172274226,3	K562	blood:
21	chr2:171092275..171093118-chr2:172272365..172273194,2	K562	blood:
22	chr2:172270508..172272587-chr2:172288176..172290267,2	K562	blood:
23	chr2:171830276..171832132-chr2:172271180..172272801,2	MCF-7	breast:
24	chr2:172267543..172269824-chr2:172270765..172273272,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000123600	Chromatin interaction
ENSG00000198586	Chromatin interaction
ENSG00000115827	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs16859368	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16859371	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16859373	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16859377	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16859386	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16859390	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16859404	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16859405	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16859410	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17287497	0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs1882378	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3731984	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3795996	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55711751	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55715902	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55716501	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55974181	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56065525	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56239048	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56273218	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56302833	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57165050	0.88[EUR][1000 genomes]
rs61021737	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61502503	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6759487	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs728651	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72882347	0.87[AFR][1000 genomes]
rs72882363	0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs73021048	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73976175	0.92[EUR][1000 genomes]
rs9646734	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3382346	chr2:172062677-172363892	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172222200-172289600	Weak transcription	Gastric	stomach
2	chr2:172261600-172277800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr2:172266400-172277400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr2:172266400-172280400	Weak transcription	Esophagus	oesophagus
5	chr2:172266400-172280400	Weak transcription	Left Ventricle	heart
6	chr2:172266400-172289600	Weak transcription	Psoas Muscle	Psoas
7	chr2:172266400-172289600	Weak transcription	Right Ventricle	heart
8	chr2:172268800-172289200	Weak transcription	HSMM	muscle
9	chr2:172269000-172280400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr2:172269200-172280200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr2:172269600-172280400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr2:172269800-172273600	Weak transcription	Colon Smooth Muscle	Colon
13	chr2:172271000-172274200	Enhancers	K562	blood
14	chr2:172271200-172272800	Enhancers	Primary B cells from peripheral blood	blood
15	chr2:172272000-172272600	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr2:172272200-172272600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr2:172272200-172272600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr2:172272200-172272600	Enhancers	Primary B cells from cord blood	blood
19	chr2:172272200-172272600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr2:172272200-172272600	Enhancers	Primary T helper cells PMA-I stimulated	--
21	chr2:172272200-172272600	Enhancers	Muscle Satellite Cultured Cells	--
22	chr2:172272200-172272600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr2:172272200-172272600	Enhancers	Fetal Brain Female	brain
24	chr2:172272200-172272600	Enhancers	Stomach Smooth Muscle	stomach
25	chr2:172272200-172272600	Flanking Active TSS	GM12878-XiMat	blood
26	chr2:172272200-172272600	Enhancers	HMEC	breast
27	chr2:172272200-172272600	Enhancers	HSMMtube	muscle
28	chr2:172272200-172272600	Enhancers	NH-A	brain
29	chr2:172272200-172272600	Enhancers	NHDF-Ad	bronchial
30	chr2:172272200-172272600	Enhancers	NHEK	skin
31	chr2:172272200-172272600	Enhancers	NHLF	lung
32	chr2:172272200-172272800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr2:172272200-172272800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr2:172272200-172273000	Enhancers	Cortex derived primary cultured neurospheres	brain
35	chr2:172272200-172273000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr2:172272200-172273000	Enhancers	Liver	Liver
37	chr2:172272200-172273000	Enhancers	Fetal Intestine Small	intestine
38	chr2:172272200-172273200	Enhancers	HepG2	liver
39	chr2:172272400-172272600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr2:172272400-172272600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr2:172272400-172272600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr2:172272400-172272600	Enhancers	Primary T cells from cord blood	blood
43	chr2:172272400-172272600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
44	chr2:172272400-172272600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr2:172272400-172272600	Enhancers	Adipose Nuclei	Adipose
46	chr2:172272400-172272600	Enhancers	Brain Angular Gyrus	brain
47	chr2:172272400-172272600	Enhancers	Brain Germinal Matrix	brain
48	chr2:172272400-172272600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
49	chr2:172272400-172272600	Enhancers	Fetal Brain Male	brain
50	chr2:172272400-172272600	Enhancers	Fetal Intestine Large	intestine

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