Variant report

Variant	rs4875129
Chromosome Location	chr8:4802339-4802340
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10503295	0.89[GIH][hapmap]
rs11985845	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs11989036	1.00[CHB][hapmap]
rs11996410	0.85[MEX][hapmap]
rs11998341	0.85[MEX][hapmap]
rs12056859	0.85[MEX][hapmap]
rs12334427	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap]
rs12334743	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12334744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs12334748	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12334931	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap]
rs12541001	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12542818	0.83[MEX][hapmap]
rs13249466	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13250626	0.91[CEU][hapmap]
rs13259602	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap]
rs13269117	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs13280124	0.96[CEU][hapmap];1.00[CHB][hapmap]
rs17071982	1.00[JPT][hapmap]
rs2924717	1.00[JPT][hapmap]
rs2924730	1.00[JPT][hapmap]
rs2977728	1.00[JPT][hapmap]
rs2977729	1.00[JPT][hapmap]
rs3911307	1.00[JPT][hapmap]
rs4341186	1.00[CHB][hapmap]
rs4535756	0.91[CEU][hapmap]
rs4875418	0.84[MEX][hapmap]
rs5001120	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs5001124	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs5001125	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs5001126	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs57424708	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6558944	1.00[JPT][hapmap]
rs6981938	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6982358	0.83[GIH][hapmap]
rs6990414	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6990769	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap]
rs6999675	1.00[JPT][hapmap]
rs7003760	0.82[EUR][1000 genomes]
rs7004731	0.80[EUR][1000 genomes]
rs7005814	0.81[EUR][1000 genomes]
rs7011210	1.00[CEU][hapmap]
rs7825060	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7828818	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7829151	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7840682	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap]
rs7841154	0.92[CEU][hapmap]
rs7841741	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs7842153	1.00[CEU][hapmap]
rs9657371	1.00[CHB][hapmap];1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv609876	chr8:4494811-5092970	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1029480	chr8:4497596-5081032	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv498130	chr8:4532988-5176376	Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv889976	chr8:4750266-4824335	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv1028542	chr8:4758159-4824005	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv1031026	chr8:4771072-5054326	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4875129	CLDN23	cis	parietal	SCAN
rs4875129	CSMD1	cis	cerebellum	SCAN

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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