Variant report

Variant	rs9540919
Chromosome Location	chr13:67382348-67382349
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1025850	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11616479	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11617188	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12428689	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12429996	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12860004	0.80[ASN][1000 genomes]
rs12875661	0.81[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs12875687	0.81[CEU][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs1441996	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1442004	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1442006	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1442013	0.81[CHB][hapmap]
rs1475207	0.81[CHB][hapmap]
rs1530301	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1561768	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1866983	0.81[CHB][hapmap]
rs1998607	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2010695	0.84[ASN][1000 genomes]
rs2031350	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2053497	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs2165599	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2165600	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2324967	0.81[CHB][hapmap]
rs2324988	0.81[CHB][hapmap]
rs2875502	0.81[CHB][hapmap]
rs4591020	0.81[CHB][hapmap]
rs4630424	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4883787	0.81[CHB][hapmap]
rs4884705	0.87[ASN][1000 genomes]
rs7318448	0.80[CHB][hapmap]
rs7358806	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs746273	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7986641	0.81[CHB][hapmap]
rs7993113	0.81[CHB][hapmap]
rs7994100	0.81[CHB][hapmap]
rs9285255	0.85[CHB][hapmap]
rs9317615	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9317618	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9317619	0.84[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9317620	0.88[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs9529137	0.81[CHB][hapmap]
rs9529148	0.87[ASN][1000 genomes]
rs9540911	0.81[CHB][hapmap]
rs9540920	1.00[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap]
rs9540923	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs9540936	0.84[ASN][1000 genomes]
rs9564345	0.81[CHB][hapmap]
rs9564350	0.81[CHB][hapmap]
rs9571678	0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs9571679	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9592487	0.82[AMR][1000 genomes]
rs9592488	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9592490	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9592491	0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9599147	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9599148	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9599152	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9599153	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs9599157	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs988157	0.81[CHB][hapmap]
rs9972065	0.85[CEU][hapmap];0.83[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041133	chr13:66723731-67530595	Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv530605	chr13:67126136-67697306	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv455928	chr13:67212422-67392298	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv562131	chr13:67212422-67392298	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv1035741	chr13:67212973-68077950	Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv541817	chr13:67212973-68077950	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv1042768	chr13:67276493-67416565	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv523360	chr13:67322714-67520344	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv1051576	chr13:67322747-67520255	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv900404	chr13:67325786-67392298	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv900405	chr13:67347245-67446835	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv1042756	chr13:67352439-67445867	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv430580	chr13:67352439-67468100	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	nsv562136	chr13:67355618-67485147	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv1051623	chr13:67377549-67465276	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:67375800-67383600	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr13:67380800-67383600	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr13:67380800-67384000	Weak transcription	Fetal Lung	lung
4	chr13:67381200-67383400	Weak transcription	Brain Anterior Caudate	brain
5	chr13:67381200-67383600	Weak transcription	Brain Cingulate Gyrus	brain
6	chr13:67381400-67383400	Weak transcription	Brain Substantia Nigra	brain

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