Variant report

Variant	rs6559835
Chromosome Location	chr9:72499942-72499943
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10115144	0.95[ASN][1000 genomes]
rs10117766	0.95[ASN][1000 genomes]
rs10122385	0.95[ASN][1000 genomes]
rs1027288	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10780684	0.95[ASN][1000 genomes]
rs10780685	0.95[ASN][1000 genomes]
rs10780686	0.95[ASN][1000 genomes]
rs10868224	0.95[ASN][1000 genomes]
rs10868225	0.95[ASN][1000 genomes]
rs10868227	0.95[ASN][1000 genomes]
rs10868234	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1119563	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1119564	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1389123	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1389124	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1389126	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1493055	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1586915	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1826476	0.95[ASN][1000 genomes]
rs1873823	0.95[ASN][1000 genomes]
rs1873824	0.93[ASN][1000 genomes]
rs1907960	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1907962	0.87[ASN][1000 genomes]
rs2035920	0.93[ASN][1000 genomes]
rs2035921	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2101686	0.95[ASN][1000 genomes]
rs4237236	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4258059	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4363263	0.95[ASN][1000 genomes]
rs4381006	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4381007	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4407955	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4475565	0.95[ASN][1000 genomes]
rs4548246	0.95[ASN][1000 genomes]
rs4584204	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744577	0.95[ASN][1000 genomes]
rs4744578	0.95[ASN][1000 genomes]
rs4744944	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744945	0.95[ASN][1000 genomes]
rs4744946	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744950	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744951	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744952	0.95[ASN][1000 genomes]
rs55816194	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6559830	0.95[ASN][1000 genomes]
rs6559831	0.95[ASN][1000 genomes]
rs6559841	0.95[ASN][1000 genomes]
rs6559842	0.95[ASN][1000 genomes]
rs6559843	0.95[ASN][1000 genomes]
rs7021905	0.95[ASN][1000 genomes]
rs7022703	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7025411	0.95[ASN][1000 genomes]
rs7026857	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7028323	0.95[ASN][1000 genomes]
rs7042001	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7043409	0.95[ASN][1000 genomes]
rs7043623	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7045208	0.95[ASN][1000 genomes]
rs7047265	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7465920	0.95[ASN][1000 genomes]
rs766003	0.95[ASN][1000 genomes]
rs7868466	0.95[ASN][1000 genomes]
rs7875361	0.95[ASN][1000 genomes]
rs9285051	0.95[ASN][1000 genomes]
rs990865	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050920	chr9:72345297-72579301	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv831611	chr9:72361905-72512134	Weak transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv893438	chr9:72363992-72720438	Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv831612	chr9:72473778-72634253	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv471310	chr9:72479046-72508302	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv614580	chr9:72479046-72508302	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv466416	chr9:72479046-72513240	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv614581	chr9:72479046-72513240	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72497200-72500400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr9:72498400-72506800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr9:72498600-72500400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr9:72499200-72500000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr9:72499200-72501200	Enhancers	Psoas Muscle	Psoas
6	chr9:72499200-72501600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr9:72499200-72501800	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr9:72499200-72502200	Enhancers	HMEC	breast
9	chr9:72499400-72505400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr9:72499800-72500600	Enhancers	A549	lung
11	chr9:72499800-72501600	Enhancers	Hela-S3	cervix
12	chr9:72499800-72501600	Enhancers	HUVEC	blood vessel
13	chr9:72499800-72501600	Enhancers	NHEK	skin

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