Variant report

Variant	rs6869329
Chromosome Location	chr5:2085954-2085955
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 77 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10039186	0.86[AFR][1000 genomes]
rs10039370	0.82[AFR][1000 genomes]
rs10039392	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10039393	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10062706	0.96[ASN][1000 genomes]
rs10063808	0.83[LWK][hapmap];0.94[MKK][hapmap];0.88[YRI][hapmap]
rs10066240	0.82[AFR][1000 genomes]
rs10066385	0.82[AFR][1000 genomes]
rs10066597	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10067919	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10068233	0.82[AFR][1000 genomes]
rs10068634	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10068847	0.81[AFR][1000 genomes]
rs10073733	0.86[AFR][1000 genomes]
rs10075502	0.81[AFR][1000 genomes]
rs10076573	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11133925	0.81[ASN][1000 genomes]
rs11741616	0.82[AFR][1000 genomes]
rs11741646	0.82[AFR][1000 genomes]
rs12054704	0.91[ASN][1000 genomes]
rs12054740	0.88[ASN][1000 genomes]
rs12055227	0.88[ASN][1000 genomes]
rs13357993	0.89[MKK][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes]
rs13357995	0.82[YRI][hapmap];0.82[AFR][1000 genomes]
rs13358958	0.82[AFR][1000 genomes]
rs4246755	0.81[ASN][1000 genomes]
rs4299769	0.90[ASN][1000 genomes]
rs4361563	0.83[ASN][1000 genomes]
rs4568402	0.91[ASN][1000 genomes]
rs55637118	1.00[ASN][1000 genomes]
rs55637204	1.00[ASN][1000 genomes]
rs55719457	1.00[ASN][1000 genomes]
rs55791921	1.00[ASN][1000 genomes]
rs55920103	1.00[ASN][1000 genomes]
rs56125143	0.83[ASN][1000 genomes]
rs56130408	1.00[ASN][1000 genomes]
rs56173153	1.00[ASN][1000 genomes]
rs56186338	1.00[ASN][1000 genomes]
rs56188011	1.00[ASN][1000 genomes]
rs56277896	1.00[ASN][1000 genomes]
rs56292928	0.91[ASN][1000 genomes]
rs56365450	1.00[ASN][1000 genomes]
rs56408053	0.95[ASN][1000 genomes]
rs58739107	1.00[ASN][1000 genomes]
rs59104705	1.00[ASN][1000 genomes]
rs59337987	1.00[ASN][1000 genomes]
rs59685893	1.00[ASN][1000 genomes]
rs60006209	1.00[ASN][1000 genomes]
rs60697393	1.00[ASN][1000 genomes]
rs61623125	1.00[ASN][1000 genomes]
rs61659441	0.83[AFR][1000 genomes]
rs62327939	0.86[AFR][1000 genomes]
rs6869000	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6893206	0.87[ASN][1000 genomes]
rs72708663	0.93[ASN][1000 genomes]
rs72708679	1.00[ASN][1000 genomes]
rs72708681	1.00[ASN][1000 genomes]
rs72708682	0.98[ASN][1000 genomes]
rs72708684	1.00[ASN][1000 genomes]
rs72708689	1.00[ASN][1000 genomes]
rs72708693	1.00[ASN][1000 genomes]
rs72708694	1.00[ASN][1000 genomes]
rs72708697	1.00[ASN][1000 genomes]
rs72708698	1.00[ASN][1000 genomes]
rs72708699	1.00[ASN][1000 genomes]
rs72708702	1.00[ASN][1000 genomes]
rs72710605	0.91[ASN][1000 genomes]
rs73732562	0.86[AFR][1000 genomes]
rs7702195	0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.94[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	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	nsv1032759	chr5:2044117-2091631	Enhancers Strong transcription Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1020211	chr5:2045699-2104887	Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv523478	chr5:2075162-2091155	Enhancers ZNF genes & repeats Weak transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6869329	SLC9A3	cis	parietal	SCAN
rs6869329	SLC6A18	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:2085200-2086000	Enhancers	iPS-20b Cell Line	embryonic stem cell
2	chr5:2085600-2087200	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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