Variant report

Variant	rs309940
Chromosome Location	chr5:42926377-42926378
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:42924589..42926644-chr5:42983759..42986055,2	MCF-7	breast:

Extended variants
information (count: 78 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10036916	0.83[ASN][1000 genomes]
rs10941595	0.87[EUR][1000 genomes]
rs10941597	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs10941598	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11743123	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11743246	0.82[EUR][1000 genomes]
rs11747714	0.83[ASN][1000 genomes]
rs11949444	0.87[EUR][1000 genomes]
rs11951144	0.97[EUR][1000 genomes]
rs11954543	0.81[EUR][1000 genomes]
rs11958520	0.86[EUR][1000 genomes]
rs12153132	0.84[EUR][1000 genomes]
rs12187928	0.87[EUR][1000 genomes]
rs13156722	0.87[EUR][1000 genomes]
rs13185118	0.87[EUR][1000 genomes]
rs17300176	0.98[ASN][1000 genomes]
rs186324	0.81[ASN][1000 genomes]
rs188693	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2247280	0.96[ASN][1000 genomes]
rs2432097	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2548334	0.81[ASN][1000 genomes]
rs2548336	0.80[ASN][1000 genomes]
rs2548373	0.96[ASN][1000 genomes]
rs2548374	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2548382	0.93[CEU][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2603625	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2603626	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2603627	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2603628	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2603629	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2603630	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2603631	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2603632	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2603633	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2603634	0.96[ASN][1000 genomes]
rs2603644	0.82[ASN][1000 genomes]
rs2603649	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2603650	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2882295	0.81[ASN][1000 genomes]
rs2924817	0.94[ASN][1000 genomes]
rs309911	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs309912	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs309923	0.89[YRI][hapmap]
rs309938	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs309939	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs309948	0.81[ASN][1000 genomes]
rs309950	0.83[ASN][1000 genomes]
rs34009007	0.87[EUR][1000 genomes]
rs36171678	0.83[EUR][1000 genomes]
rs3849696	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3849697	0.83[ASN][1000 genomes]
rs3909456	0.82[CHB][hapmap];0.83[ASN][1000 genomes]
rs6859096	0.82[EUR][1000 genomes]
rs6861491	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6880163	0.84[ASN][1000 genomes]
rs6882794	0.80[ASN][1000 genomes]
rs6883097	0.84[ASN][1000 genomes]
rs6884740	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6889150	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6889271	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6890457	0.93[CHB][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6890469	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6895732	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6899257	0.83[ASN][1000 genomes]
rs7733383	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv993554	chr5:42720939-43251863	Bivalent/Poised TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	298 gene(s)	inside rSNPs	diseases
2	nsv462126	chr5:42728831-43237188	Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
3	nsv597925	chr5:42728831-43237188	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
4	nsv1023741	chr5:42768215-43348145	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
5	nsv537737	chr5:42768215-43348145	Genic enhancers Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
6	nsv534185	chr5:42804840-43067088	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	165 gene(s)	inside rSNPs	diseases
7	nsv1018276	chr5:42809131-42975245	Strong transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv980936	chr5:42894375-42930741	Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv968909	chr5:42903982-42953465	Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
10	esv1806082	chr5:42906572-42967215	Transcr. at gene 5' and 3' Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	esv1813779	chr5:42906572-42992040	Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
12	nsv969923	chr5:42919063-42930741	Bivalent Enhancer Weak transcription Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	esv3346992	chr5:42921680-42970055	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs309940	ZNF131	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:42916000-42929400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr5:42925800-42926400	Enhancers	Primary neutrophils fromperipheralblood	blood

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