Variant report

Variant	rs57597020
Chromosome Location	chr5:43507577-43507578
allele	C/T
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:43505860..43508968-chr5:43512640..43515485,3	MCF-7	breast:
2	chr5:43505801..43507815-chr5:43555939..43557727,2	MCF-7	breast:
3	chr5:43482924..43484837-chr5:43505826..43508408,3	MCF-7	breast:
4	chr5:43502114..43510409-chr5:43511788..43516990,15	K562	blood:
5	chr5:43497976..43500282-chr5:43507401..43510393,2	K562	blood:
6	chr5:43486106..43488978-chr5:43507270..43509825,2	K562	blood:
7	chr5:43481775..43485918-chr5:43506261..43509799,5	K562	blood:
8	chr5:43505282..43507808-chr5:43556089..43557593,2	K562	blood:
9	chr5:43482757..43485165-chr5:43504777..43508621,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000172239	Chromatin interaction
ENSG00000249492	Chromatin interaction
ENSG00000248240	Chromatin interaction
ENSG00000172244	Chromatin interaction
ENSG00000151881	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10036954	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10038608	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10042992	0.87[EUR][1000 genomes]
rs10045400	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10045455	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10058558	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10061165	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10074682	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10447144	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10462051	0.87[EUR][1000 genomes]
rs10473311	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10941640	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12332560	0.88[EUR][1000 genomes]
rs12651879	0.88[EUR][1000 genomes]
rs12659369	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12697452	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13185343	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13189004	0.88[EUR][1000 genomes]
rs13360902	0.82[ASN][1000 genomes]
rs1389868	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1389869	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1428640	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2013173	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2131999	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2132000	0.91[EUR][1000 genomes]
rs2172763	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34007811	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35710460	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35881272	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36013953	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3776423	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3806870	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4073848	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4073850	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4073851	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4242099	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4308491	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4331909	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4367306	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4415083	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4467713	0.89[EUR][1000 genomes]
rs4513704	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4541663	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4576155	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4866746	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4866833	0.92[EUR][1000 genomes]
rs55641556	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56400900	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57547662	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6451692	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6451693	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6451695	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6451696	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6451698	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6451703	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6451704	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6451706	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6451712	0.89[EUR][1000 genomes]
rs67466542	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs67581152	0.87[EUR][1000 genomes]
rs6858942	0.87[EUR][1000 genomes]
rs6859344	0.81[EUR][1000 genomes]
rs6861704	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6862102	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6865217	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6870018	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6870783	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6883661	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73100614	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs750582	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs750584	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7703662	0.80[AMR][1000 genomes]
rs7707976	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7708369	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7708443	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7717636	0.88[EUR][1000 genomes]
rs7724571	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7731091	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7734393	0.90[EUR][1000 genomes]
rs7735243	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9292883	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9686159	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9687341	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9885467	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881017	chr5:43444826-43731692	Weak transcription Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	222 gene(s)	inside rSNPs	diseases
2	nsv830275	chr5:43469511-43639384	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	220 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43484800-43511000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr5:43484800-43514000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr5:43484800-43514600	Weak transcription	Ovary	ovary
4	chr5:43484800-43514800	Weak transcription	Spleen	Spleen
5	chr5:43485000-43513400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr5:43485000-43513800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr5:43485000-43514200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr5:43485200-43513200	Weak transcription	NHDF-Ad	bronchial
9	chr5:43485200-43513200	Weak transcription	NHLF	lung
10	chr5:43485200-43513400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr5:43485200-43513400	Weak transcription	Fetal Lung	lung
12	chr5:43485200-43513600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr5:43485200-43513600	Weak transcription	Fetal Intestine Small	intestine
14	chr5:43485200-43513600	Weak transcription	HSMM	muscle
15	chr5:43485200-43513600	Weak transcription	NH-A	brain
16	chr5:43485200-43514200	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr5:43485400-43514200	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr5:43485800-43514200	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr5:43486000-43509800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr5:43486000-43514200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr5:43486400-43513400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr5:43486400-43513600	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr5:43486800-43512200	Weak transcription	HepG2	liver
24	chr5:43486800-43513400	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr5:43487400-43510800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr5:43487600-43513600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr5:43490400-43513600	Weak transcription	Primary B cells from cord blood	blood
28	chr5:43492000-43514600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr5:43495000-43513000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr5:43495000-43514600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr5:43496400-43510000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr5:43498000-43509600	Strong transcription	Dnd41	blood
33	chr5:43498200-43513800	Weak transcription	Duodenum Mucosa	Duodenum
34	chr5:43498200-43514000	Weak transcription	Rectal Smooth Muscle	rectum
35	chr5:43498200-43514200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr5:43498200-43514200	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr5:43498400-43513600	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr5:43499400-43513600	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr5:43499400-43514600	Weak transcription	Left Ventricle	heart
40	chr5:43499800-43514600	Weak transcription	Aorta	Aorta
41	chr5:43500000-43513400	Weak transcription	Fetal Heart	heart
42	chr5:43500800-43509600	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr5:43501200-43509400	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr5:43501600-43513600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr5:43501600-43514200	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr5:43502000-43513600	Weak transcription	Fetal Kidney	kidney
47	chr5:43502200-43509200	Strong transcription	Fetal Thymus	thymus
48	chr5:43502200-43513600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr5:43502200-43514600	Weak transcription	Esophagus	oesophagus
50	chr5:43502600-43509200	Strong transcription	iPS-20b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links