Variant report

Variant	rs2697548
Chromosome Location	chr5:90330959-90330960
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10037172	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1818349	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1830364	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2367279	0.81[CHB][hapmap];0.90[CHD][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs2367284	0.84[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs2697542	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.90[TSI][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2973446	0.89[CEU][hapmap];0.93[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs4244206	0.89[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7449334	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9293558	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs937920	0.91[ASW][hapmap];0.92[LWK][hapmap];0.87[MKK][hapmap];0.91[YRI][hapmap];0.90[AFR][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:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:90323600-90332800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr5:90324200-90332800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr5:90324200-90332800	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr5:90324600-90335200	Weak transcription	Small Intestine	intestine
5	chr5:90324600-90350400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr5:90329400-90331200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr5:90329400-90333600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr5:90329600-90333600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr5:90329600-90334200	Weak transcription	Psoas Muscle	Psoas
10	chr5:90330400-90331000	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr5:90330400-90331000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr5:90330400-90331000	Enhancers	Colon Smooth Muscle	Colon
13	chr5:90330400-90331200	Enhancers	Rectal Smooth Muscle	rectum
14	chr5:90330600-90331000	Enhancers	H1 Cell Line	embryonic stem cell
15	chr5:90330800-90332800	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr5:90330800-90333000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr5:90330800-90333400	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr5:90330800-90338000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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