Variant report

Variant	rs13339408
Chromosome Location	chr16:76374438-76374439
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:76373071..76375700-chr16:76381006..76383022,2	MCF-7	breast:

Extended variants
information (count: 135 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs1035531	0.93[CEU][hapmap];0.99[EUR][1000 genomes]
rs1035532	0.84[ASW][hapmap];0.86[CEU][hapmap];0.95[GIH][hapmap];0.88[LWK][hapmap];1.00[TSI][hapmap];0.89[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs11149892	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11149893	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11865582	0.91[CHB][hapmap];0.82[ASN][1000 genomes]
rs11865753	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12325009	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12325294	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12325365	0.90[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12325498	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12325501	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12595966	0.88[ASN][1000 genomes]
rs12596487	0.95[CHB][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs12596963	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs12597029	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12597605	0.88[ASN][1000 genomes]
rs12597720	0.88[ASN][1000 genomes]
rs12600063	0.95[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs12716807	0.95[CHB][hapmap];0.80[ASN][1000 genomes]
rs12716808	0.95[CHB][hapmap];0.80[ASN][1000 genomes]
rs12924602	0.80[ASN][1000 genomes]
rs12924751	0.95[CHB][hapmap];0.80[ASN][1000 genomes]
rs12926384	0.80[ASN][1000 genomes]
rs12930160	0.95[CHB][hapmap];0.80[ASN][1000 genomes]
rs13332281	0.86[CHB][hapmap]
rs13333980	0.93[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1346554	0.88[ASN][1000 genomes]
rs1346555	0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs1346556	0.91[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs1346557	1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.94[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1428753	0.95[CHB][hapmap]
rs1549661	0.93[CEU][hapmap];0.99[EUR][1000 genomes]
rs1559329	0.93[CEU][hapmap];0.99[EUR][1000 genomes]
rs16944192	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs16944222	0.95[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs16944228	0.93[CEU][hapmap];0.99[EUR][1000 genomes]
rs17698942	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17698959	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17698989	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17698995	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17699048	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17699107	0.88[ASN][1000 genomes]
rs17699131	0.89[ASN][1000 genomes]
rs17699142	0.89[ASN][1000 genomes]
rs17699214	0.95[CHB][hapmap];0.84[CHD][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs17699220	0.91[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs17699232	0.82[ASN][1000 genomes]
rs17766465	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17766542	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17766704	0.95[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs17766740	0.91[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs17766856	0.86[ASN][1000 genomes]
rs17766862	0.95[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs17766904	0.87[CHB][hapmap];0.84[CHD][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs1964297	0.86[CEU][hapmap];0.80[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs2115387	0.88[EUR][1000 genomes]
rs2195428	0.94[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs2195429	0.95[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs2216743	0.93[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28417722	0.88[ASN][1000 genomes]
rs2866713	0.95[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs2866714	0.95[CHB][hapmap];0.84[CHD][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs34176229	0.82[ASN][1000 genomes]
rs34500194	0.88[ASN][1000 genomes]
rs35538603	0.87[EUR][1000 genomes]
rs4448976	0.87[ASN][1000 genomes]
rs4528602	0.95[CHB][hapmap];0.84[CHD][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs4595825	0.95[CHB][hapmap];0.84[CHD][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs58234937	0.89[ASN][1000 genomes]
rs58799953	0.99[EUR][1000 genomes]
rs59062545	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59071741	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59708157	0.88[ASN][1000 genomes]
rs60730550	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61147122	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61245681	0.90[ASN][1000 genomes]
rs61368169	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66508951	0.84[ASN][1000 genomes]
rs7184662	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7187266	0.95[CHB][hapmap];0.80[ASN][1000 genomes]
rs7193350	0.91[CHB][hapmap];0.85[CHD][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs7204781	0.93[CEU][hapmap];0.99[EUR][1000 genomes]
rs72626197	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72626198	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72626199	0.96[ASN][1000 genomes]
rs72626200	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72626201	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72626202	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72628203	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72628204	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72628206	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72628207	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72628208	0.91[ASN][1000 genomes]
rs72628209	0.91[ASN][1000 genomes]
rs72628210	0.88[ASN][1000 genomes]
rs72628211	0.88[ASN][1000 genomes]
rs72628212	0.88[ASN][1000 genomes]
rs72628213	0.86[ASN][1000 genomes]
rs72628214	0.84[ASN][1000 genomes]
rs72628215	0.84[ASN][1000 genomes]
rs72628216	0.84[ASN][1000 genomes]
rs7501035	0.95[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs8043911	0.86[ASN][1000 genomes]
rs8045505	0.95[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs8045699	0.91[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs8045862	0.91[ASN][1000 genomes]
rs8046953	0.81[CEU][hapmap];0.90[GIH][hapmap];0.92[TSI][hapmap];0.96[EUR][1000 genomes]
rs8047690	0.91[ASN][1000 genomes]
rs8049390	0.99[EUR][1000 genomes]
rs8049902	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8059413	0.87[ASN][1000 genomes]
rs8062657	0.86[ASN][1000 genomes]
rs8062793	0.86[ASN][1000 genomes]
rs8063803	0.86[ASN][1000 genomes]
rs9319495	0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9921874	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs9924992	0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs9934361	0.91[CHB][hapmap]
rs9937260	0.95[CHB][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064607	chr16:75787129-76449101	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv1065794	chr16:75792288-76434118	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv542961	chr16:75792288-76434118	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv1059162	chr16:75929348-76730816	Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv572995	chr16:75935025-76708417	Enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv572996	chr16:75935025-76735249	Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv817220	chr16:75939705-76735383	ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv1056021	chr16:75955522-76729765	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
9	nsv542962	chr16:75955522-76729765	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
10	nsv906935	chr16:76031737-76453110	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv906936	chr16:76031737-76768178	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
12	nsv817549	chr16:76067068-76582099	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
13	nsv1065644	chr16:76166579-76475634	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
14	nsv869200	chr16:76227867-76695732	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
15	nsv833286	chr16:76243730-76444283	Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
16	esv2763142	chr16:76271660-76461841	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats 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
rs13339408	CNTNAP4	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:76369800-76376800	Weak transcription	Brain Cingulate Gyrus	brain
2	chr16:76370000-76378800	Weak transcription	Brain Hippocampus Middle	brain
3	chr16:76370000-76378800	Weak transcription	Brain Substantia Nigra	brain
4	chr16:76370000-76379000	Weak transcription	Brain Anterior Caudate	brain
5	chr16:76373800-76374600	Enhancers	H1 Cell Line	embryonic stem cell
6	chr16:76374000-76377200	Weak transcription	Brain Germinal Matrix	brain
7	chr16:76374200-76383000	Weak transcription	Brain Angular Gyrus	brain

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