Variant report

Variant	rs2662279
Chromosome Location	chr5:90333141-90333142
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:90332679..90335519-chr5:90676222..90679185,2	K562	blood:
2	chr5:90289665..90292276-chr5:90332798..90334401,2	MCF-7	breast:
3	chr5:90331219..90333780-chr5:90335646..90338696,3	K562	blood:
4	chr5:90331134..90333173-chr5:90336789..90338560,2	K562	blood:

Variant related genes	Relation type
ENSG00000113369	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10942624	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12186662	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs13179479	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13180409	0.95[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1819073	0.91[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1819074	0.91[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1828177	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1828178	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1848486	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1848487	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1852734	0.95[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1858070	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2048217	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2367186	0.99[ASN][1000 genomes]
rs2367274	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2463775	1.00[CEU][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2662278	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2662280	0.95[CEU][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes]
rs2662281	0.91[ASN][1000 genomes]
rs2662282	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2662283	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2662284	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2697543	0.95[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2697544	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2697546	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28875340	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4254936	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4454077	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6452930	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6452934	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6452935	0.82[AMR][1000 genomes]
rs6865615	0.91[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap]
rs6882081	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs689544	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7706034	0.91[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7719311	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7723511	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7733230	0.91[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs937920	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs998788	1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529544	chr5:89523963-90412409	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv882369	chr5:90275825-90344149	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1024813	chr5:90321535-90870739	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
4	nsv537806	chr5:90321535-90870739	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:90324600-90335200	Weak transcription	Small Intestine	intestine
2	chr5:90324600-90350400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr5:90329400-90333600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr5:90329600-90333600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr5:90329600-90334200	Weak transcription	Psoas Muscle	Psoas
6	chr5:90330800-90333400	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr5:90330800-90338000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr5:90331000-90333600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr5:90331800-90334000	Weak transcription	Fetal Stomach	stomach
10	chr5:90332800-90333400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr5:90332800-90334200	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr5:90332800-90334600	Enhancers	H9 Cell Line	embryonic stem cell
13	chr5:90332800-90335400	Enhancers	Colon Smooth Muscle	Colon
14	chr5:90332800-90335400	Enhancers	Rectal Smooth Muscle	rectum
15	chr5:90333000-90333200	Enhancers	Sigmoid Colon	Sigmoid Colon
16	chr5:90333000-90333400	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr5:90333000-90333400	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr5:90333000-90333800	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr5:90333000-90334000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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