Variant report

Variant	rs4960969
Chromosome Location	chr8:90323764-90323765
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 102 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10086145	0.94[EUR][1000 genomes]
rs10086662	0.91[EUR][1000 genomes]
rs10086804	0.91[EUR][1000 genomes]
rs10086889	0.91[EUR][1000 genomes]
rs10087030	0.91[EUR][1000 genomes]
rs10089719	0.91[EUR][1000 genomes]
rs10101424	0.90[EUR][1000 genomes]
rs10101786	0.90[EUR][1000 genomes]
rs10102049	0.94[EUR][1000 genomes]
rs10104434	0.90[EUR][1000 genomes]
rs10104777	0.90[EUR][1000 genomes]
rs10107649	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10111636	0.86[EUR][1000 genomes]
rs1011271	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1037333	0.84[EUR][1000 genomes]
rs1038160	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10504876	0.92[EUR][1000 genomes]
rs1114316	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11785662	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11785864	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12547059	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12549342	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13252577	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13254433	0.85[EUR][1000 genomes]
rs13259581	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13262086	0.94[EUR][1000 genomes]
rs13262488	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13273491	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13276440	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13278618	0.94[EUR][1000 genomes]
rs13279324	0.93[EUR][1000 genomes]
rs1383035	0.95[EUR][1000 genomes]
rs1383036	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1383037	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1383038	0.82[ASN][1000 genomes]
rs1479898	0.94[EUR][1000 genomes]
rs1479909	0.91[EUR][1000 genomes]
rs1479911	0.91[EUR][1000 genomes]
rs1600505	0.93[EUR][1000 genomes]
rs1600506	0.93[EUR][1000 genomes]
rs16893960	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1824967	0.95[EUR][1000 genomes]
rs1842297	0.95[EUR][1000 genomes]
rs2068088	0.96[EUR][1000 genomes]
rs2198094	0.94[EUR][1000 genomes]
rs2219864	0.96[EUR][1000 genomes]
rs2338697	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2879240	0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35369616	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35981062	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36072714	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4246119	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4266696	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4268168	0.96[EUR][1000 genomes]
rs4291311	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4302887	0.81[EUR][1000 genomes]
rs4380986	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4493948	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4506265	0.91[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes]
rs4509384	0.96[EUR][1000 genomes]
rs4568650	0.91[EUR][1000 genomes]
rs4588905	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4960970	0.90[EUR][1000 genomes]
rs4961128	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4961129	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55822643	0.91[EUR][1000 genomes]
rs58699294	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6469976	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6983174	0.85[EUR][1000 genomes]
rs6989492	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6990609	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7012184	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7014069	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72665939	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7817287	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7818117	0.92[EUR][1000 genomes]
rs7818636	0.94[EUR][1000 genomes]
rs7820067	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7821252	0.95[EUR][1000 genomes]
rs7826977	0.83[CHB][hapmap];0.86[JPT][hapmap];0.87[EUR][1000 genomes]
rs7828790	0.83[CHB][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes]
rs7835780	0.91[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs7837196	0.93[EUR][1000 genomes]
rs7837625	0.94[EUR][1000 genomes]
rs7840648	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7843823	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8180941	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9656807	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9656936	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs989108	0.91[CEU][hapmap];0.85[JPT][hapmap];0.94[EUR][1000 genomes]
rs999542	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs999543	0.92[EUR][1000 genomes]
rs999544	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv465735	chr8:89760311-90729507	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv611714	chr8:89760311-90729507	Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Weak transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv1024956	chr8:90104423-90459539	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv539671	chr8:90104423-90459539	Active TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv1032886	chr8:90253748-90398240	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
6	nsv891178	chr8:90289326-90337010	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
7	nsv891179	chr8:90307652-90335826	Enhancers Active TSS Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
8	esv2757280	chr8:90321647-90338278	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
9	esv2759627	chr8:90321647-90338278	Weak transcription Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4960969	CA2	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:90320800-90324800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr8:90321200-90325000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr8:90321400-90324800	Weak transcription	NHEK	skin
4	chr8:90321600-90324800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr8:90321600-90324800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr8:90321600-90325000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr8:90321600-90325200	Weak transcription	Primary hematopoietic stem cells	blood
8	chr8:90323400-90323800	Enhancers	A549	lung
9	chr8:90323400-90326600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr8:90323400-90327600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr8:90323600-90323800	Enhancers	Fetal Kidney	kidney

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