Variant report

Variant	rs1601641
Chromosome Location	chr5:1987633-1987634
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10035144	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10041900	0.82[CEU][hapmap]
rs10043083	1.00[ASN][1000 genomes]
rs10045683	0.92[ASN][1000 genomes]
rs1017924	0.91[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs1023980	0.89[CEU][hapmap]
rs1023981	0.89[CEU][hapmap];0.90[GIH][hapmap]
rs10474733	0.92[ASN][1000 genomes]
rs10474734	0.92[ASN][1000 genomes]
rs10475126	0.87[EUR][1000 genomes]
rs10475128	0.88[EUR][1000 genomes]
rs11133918	0.90[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs11133920	0.88[EUR][1000 genomes]
rs1123381	0.89[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1123390	0.92[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1123391	0.92[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11749073	0.92[ASN][1000 genomes]
rs11952205	0.86[ASN][1000 genomes]
rs12188545	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12716127	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13166888	0.92[ASN][1000 genomes]
rs1486937	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3902820	1.00[ASN][1000 genomes]
rs4246752	0.81[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs4263538	0.87[EUR][1000 genomes]
rs4371796	0.92[ASN][1000 genomes]
rs4398680	0.88[ASN][1000 genomes]
rs4407661	0.91[ASN][1000 genomes]
rs4526149	1.00[ASN][1000 genomes]
rs4975775	0.85[GIH][hapmap]
rs4975777	0.91[ASN][1000 genomes]
rs4975779	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4975786	0.92[ASN][1000 genomes]
rs55860207	0.81[ASN][1000 genomes]
rs57434783	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61656301	0.87[ASN][1000 genomes]
rs62337135	0.87[ASN][1000 genomes]
rs67659713	0.90[ASN][1000 genomes]
rs6870127	0.88[EUR][1000 genomes]
rs9312970	0.92[ASN][1000 genomes]
rs965276	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv817407	chr5:1495354-2191460	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	107 gene(s)	inside rSNPs	diseases
2	nsv869236	chr5:1719263-2259100	Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
3	nsv915846	chr5:1891098-2167677	Active TSS Genic enhancers Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1026930	chr5:1898993-2126061	Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv427705	chr5:1950467-2115059	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv4681	chr5:1967628-2010091	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1601641	SLC6A18	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:1977200-1997000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr5:1987600-1987800	Bivalent Enhancer	Fetal Muscle Leg	muscle

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