Variant report

Variant	rs1005622
Chromosome Location	chr5:54172727-54172728
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10040872	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10042734	0.84[ASN][1000 genomes]
rs10056452	0.90[ASN][1000 genomes]
rs10940430	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10940431	0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10940432	0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10940434	0.93[ASN][1000 genomes]
rs11738151	0.92[ASN][1000 genomes]
rs11742711	0.89[ASN][1000 genomes]
rs11953607	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12657845	0.89[ASN][1000 genomes]
rs13181749	0.90[ASN][1000 genomes]
rs1560165	0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1560166	0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1560167	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1988528	0.81[EUR][1000 genomes]
rs1991498	0.87[CEU][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2017082	0.82[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2017318	0.81[EUR][1000 genomes]
rs2017540	0.81[EUR][1000 genomes]
rs2019005	0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2195392	0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2195393	0.86[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2407758	0.81[EUR][1000 genomes]
rs28564901	0.92[ASN][1000 genomes]
rs3916738	0.84[ASN][1000 genomes]
rs4242050	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4320216	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4502767	0.90[ASN][1000 genomes]
rs4865586	0.85[GIH][hapmap];0.89[TSI][hapmap]
rs4865879	0.90[ASN][1000 genomes]
rs4865880	0.90[ASN][1000 genomes]
rs4865881	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4865882	0.92[ASN][1000 genomes]
rs4865883	0.81[EUR][1000 genomes]
rs6860824	0.85[GIH][hapmap];0.89[TSI][hapmap]
rs737526	0.86[ASN][1000 genomes]
rs7709516	0.82[ASN][1000 genomes]
rs981978	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830300	chr5:54056300-54257344	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	esv3358092	chr5:54077828-54189150	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv598179	chr5:54156269-54192823	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:54168600-54175600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:54170000-54178800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr5:54170800-54175800	Weak transcription	NHEK	skin
4	chr5:54171400-54172800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr5:54171400-54173000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr5:54171400-54176000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr5:54172200-54173400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr5:54172400-54172800	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr5:54172400-54172800	Enhancers	Pancreas	Pancrea
10	chr5:54172400-54173000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
11	chr5:54172400-54173000	Enhancers	Fetal Intestine Small	intestine
12	chr5:54172400-54173200	Enhancers	H1 Cell Line	embryonic stem cell
13	chr5:54172400-54173200	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr5:54172400-54173200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr5:54172400-54173400	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr5:54172400-54173400	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr5:54172400-54173400	Enhancers	iPS-20b Cell Line	embryonic stem cell
18	chr5:54172400-54173600	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr5:54172600-54173200	Enhancers	Hela-S3	cervix
20	chr5:54172600-54173400	Enhancers	iPS-18 Cell Line	embryonic stem cell
21	chr5:54172600-54173400	Enhancers	Stomach Mucosa	stomach

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