Variant report

Variant	rs2662280
Chromosome Location	chr5:90329458-90329459
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10942624	0.82[EUR][1000 genomes]
rs13179479	0.90[EUR][1000 genomes]
rs13180409	0.91[CEU][hapmap];0.90[GIH][hapmap];0.82[EUR][1000 genomes]
rs1819073	0.86[CEU][hapmap];0.80[EUR][1000 genomes]
rs1819074	0.86[CEU][hapmap];0.80[EUR][1000 genomes]
rs1828177	0.86[JPT][hapmap]
rs1828178	0.86[JPT][hapmap]
rs1848486	0.95[CEU][hapmap];0.82[JPT][hapmap];0.90[EUR][1000 genomes]
rs1848487	0.95[CEU][hapmap];0.82[JPT][hapmap];0.90[EUR][1000 genomes]
rs1852734	0.91[CEU][hapmap];0.88[GIH][hapmap];0.84[EUR][1000 genomes]
rs1858070	0.86[JPT][hapmap]
rs2048217	0.86[JPT][hapmap]
rs2367274	0.82[EUR][1000 genomes]
rs2463775	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs2662278	0.84[EUR][1000 genomes]
rs2662279	0.95[CEU][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes]
rs2662282	0.92[EUR][1000 genomes]
rs2662283	0.95[CEU][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.91[EUR][1000 genomes]
rs2662284	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs2697543	0.91[CEU][hapmap];0.92[GIH][hapmap];0.84[EUR][1000 genomes]
rs2697544	0.82[EUR][1000 genomes]
rs2697546	0.95[CEU][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.82[TSI][hapmap];0.91[EUR][1000 genomes]
rs28875340	0.89[EUR][1000 genomes]
rs4254936	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs4454077	0.82[EUR][1000 genomes]
rs6452930	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs6452934	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs6865615	0.86[CEU][hapmap]
rs689544	0.86[JPT][hapmap]
rs7706034	0.86[CEU][hapmap];0.85[GIH][hapmap];0.80[EUR][1000 genomes]
rs7719311	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs7723511	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs7733230	0.86[CEU][hapmap]
rs937920	0.95[CEU][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs998788	0.82[JPT][hapmap]

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	chr5:90323600-90330400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:90323600-90332800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr5:90324200-90330400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr5:90324200-90332800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr5:90324200-90332800	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr5:90324600-90335200	Weak transcription	Small Intestine	intestine
7	chr5:90324600-90350400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr5:90328600-90329600	Enhancers	Colon Smooth Muscle	Colon
9	chr5:90328600-90329600	Enhancers	A549	lung
10	chr5:90328800-90330000	Enhancers	Liver	Liver
11	chr5:90329200-90329600	Enhancers	Fetal Intestine Large	intestine
12	chr5:90329200-90329600	Enhancers	Fetal Intestine Small	intestine
13	chr5:90329200-90329600	Enhancers	Psoas Muscle	Psoas
14	chr5:90329200-90329800	Enhancers	Rectal Smooth Muscle	rectum
15	chr5:90329400-90329600	Enhancers	iPS-20b Cell Line	embryonic stem cell
16	chr5:90329400-90330400	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr5:90329400-90330400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr5:90329400-90331200	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr5:90329400-90333600	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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