Variant report

Variant	rs2165600
Chromosome Location	chr13:67405465-67405466
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1025850	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11616479	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11617188	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12428689	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12429002	0.82[CHD][hapmap];0.87[GIH][hapmap]
rs12429996	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12430583	0.82[GIH][hapmap]
rs12860004	0.91[ASN][1000 genomes]
rs12875661	1.00[CHB][hapmap];0.89[JPT][hapmap];0.98[ASN][1000 genomes]
rs12875687	0.84[CHB][hapmap];0.84[JPT][hapmap];0.98[ASN][1000 genomes]
rs1441996	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1442004	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1442006	1.00[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1530301	0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];0.98[ASN][1000 genomes]
rs1561768	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1998607	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2010695	0.94[ASN][1000 genomes]
rs2031350	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2053497	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2165599	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4630424	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs4884705	0.98[ASN][1000 genomes]
rs7358806	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs746273	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9317615	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.98[TSI][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9317618	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9317619	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9317620	0.94[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs9529148	0.98[ASN][1000 genomes]
rs9540919	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]
rs9540920	1.00[CEU][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap]
rs9540923	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9540936	0.94[ASN][1000 genomes]
rs9564358	0.85[GIH][hapmap]
rs9571678	0.84[CHB][hapmap];0.84[JPT][hapmap];0.98[ASN][1000 genomes]
rs9571679	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9571680	0.81[CHD][hapmap];0.87[GIH][hapmap]
rs9592488	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9592490	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9592491	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9599147	0.81[ASN][1000 genomes]
rs9599152	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9599153	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];0.88[YRI][hapmap]
rs9599157	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9972065	0.84[CEU][hapmap];0.88[CHB][hapmap];0.89[JPT][hapmap];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	nsv455933	chr13:67392298-67437316	Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	nsv562137	chr13:67392298-67437316	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:67404400-67406200	Enhancers	Primary B cells from peripheral blood	blood
2	chr13:67404800-67406000	Enhancers	Brain Substantia Nigra	brain
3	chr13:67405000-67406000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr13:67405000-67406200	Enhancers	Primary B cells from cord blood	blood
5	chr13:67405200-67405600	Enhancers	Fetal Kidney	kidney
6	chr13:67405200-67406000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr13:67405200-67406000	Enhancers	Muscle Satellite Cultured Cells	--
8	chr13:67405200-67406000	Enhancers	HMEC	breast
9	chr13:67405200-67406000	Enhancers	HSMM	muscle
10	chr13:67405200-67406200	Enhancers	Brain Angular Gyrus	brain
11	chr13:67405200-67406200	Enhancers	Brain Anterior Caudate	brain
12	chr13:67405200-67406200	Enhancers	Brain Hippocampus Middle	brain
13	chr13:67405200-67406200	Enhancers	Brain Inferior Temporal Lobe	brain
14	chr13:67405400-67405800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr13:67405400-67405800	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr13:67405400-67405800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
17	chr13:67405400-67405800	Flanking Active TSS	A549	lung
18	chr13:67405400-67406000	Enhancers	Brain Cingulate Gyrus	brain

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