Variant report

Variant	rs10498959
Chromosome Location	chr6:87567123-87567124
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:87491790..87492456-chr6:87566446..87567164,4	MCF-7	breast:
2	chr6:86463941..86466706-chr6:87565460..87567312,2	MCF-7	breast:

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1013019	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12663746	1.00[ASN][1000 genomes]
rs1408447	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1535228	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16877863	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16877883	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16877984	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16877987	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16877991	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17545444	0.91[ASN][1000 genomes]
rs1884740	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2145050	0.83[ASN][1000 genomes]
rs3763231	1.00[ASN][1000 genomes]
rs4371828	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55859404	1.00[ASN][1000 genomes]
rs55982849	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56152175	0.91[ASN][1000 genomes]
rs56364606	0.91[ASN][1000 genomes]
rs62439115	1.00[ASN][1000 genomes]
rs62439116	1.00[ASN][1000 genomes]
rs62439143	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62439144	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62439145	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62439146	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62439147	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62440765	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62440766	1.00[ASN][1000 genomes]
rs62440767	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62440790	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62440822	1.00[ASN][1000 genomes]
rs6940008	0.90[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73751775	1.00[ASN][1000 genomes]
rs73751802	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9444442	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9444447	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9450536	1.00[ASN][1000 genomes]
rs9450544	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9450568	0.81[ASN][1000 genomes]
rs9450569	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9450573	0.81[ASN][1000 genomes]
rs9450587	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026234	chr6:86745200-87640200	Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv532046	chr6:86754494-87615799	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1024339	chr6:86778852-87622650	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv1018878	chr6:86778852-87691755	Enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1031639	chr6:86815397-87721507	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv1025307	chr6:87354495-87640200	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1024751	chr6:87433199-87908721	Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	esv1811101	chr6:87456503-87645214	Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	esv2758066	chr6:87456503-87645214	Enhancers Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	esv2759452	chr6:87456503-87645214	Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv1020697	chr6:87529381-87598692	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv7940	chr6:87562446-87586120	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10498959	SNX14	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:87565800-87567400	Enhancers	Ovary	ovary
2	chr6:87567000-87567600	Enhancers	Fetal Lung	lung

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