Variant report

Variant	rs12405761
Chromosome Location	chr1:57850914-57850915
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 120 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs10047071	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10047072	0.93[ASN][1000 genomes]
rs10047073	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10047177	0.95[ASN][1000 genomes]
rs10047179	0.92[ASN][1000 genomes]
rs10493219	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10493225	0.86[JPT][hapmap]
rs10889034	0.86[JPT][hapmap]
rs10889037	0.90[CHB][hapmap];0.83[ASN][1000 genomes]
rs10889039	0.82[ASN][1000 genomes]
rs10889040	0.82[ASN][1000 genomes]
rs10889041	0.80[CHB][hapmap];0.93[ASN][1000 genomes]
rs10889044	1.00[JPT][hapmap]
rs11207010	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs11207011	0.86[JPT][hapmap]
rs11207017	0.83[ASN][1000 genomes]
rs11207018	0.82[ASN][1000 genomes]
rs11207020	0.86[ASN][1000 genomes]
rs11207021	0.88[ASN][1000 genomes]
rs11207022	0.81[ASN][1000 genomes]
rs11207027	0.86[JPT][hapmap]
rs11579258	0.88[ASN][1000 genomes]
rs11581250	0.88[ASN][1000 genomes]
rs11585284	0.88[ASN][1000 genomes]
rs11585751	1.00[JPT][hapmap]
rs11586826	0.88[ASN][1000 genomes]
rs11590652	0.91[ASN][1000 genomes]
rs11590708	0.80[CHB][hapmap]
rs12044912	0.86[JPT][hapmap]
rs12046102	0.86[JPT][hapmap]
rs12061812	0.86[JPT][hapmap]
rs12067263	0.93[ASN][1000 genomes]
rs12085326	0.85[ASN][1000 genomes]
rs12087888	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs12119147	0.90[CHB][hapmap];0.82[ASN][1000 genomes]
rs12124445	0.88[ASN][1000 genomes]
rs12125219	0.88[ASN][1000 genomes]
rs12126723	0.80[CHB][hapmap]
rs12127603	0.88[ASN][1000 genomes]
rs12128305	0.86[JPT][hapmap]
rs12132685	0.86[JPT][hapmap]
rs12136107	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12137169	1.00[JPT][hapmap]
rs12137540	0.89[ASN][1000 genomes]
rs12142821	0.86[JPT][hapmap]
rs12240237	0.80[CHB][hapmap]
rs1240442	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1240443	0.93[ASN][1000 genomes]
rs12565446	0.80[CHB][hapmap]
rs12566690	0.86[ASN][1000 genomes]
rs12568449	0.85[JPT][hapmap]
rs12726704	1.00[JPT][hapmap]
rs12741210	0.91[CHB][hapmap];0.83[ASN][1000 genomes]
rs12752978	0.86[JPT][hapmap]
rs1334239	0.86[JPT][hapmap]
rs1334240	0.86[JPT][hapmap]
rs1424463	0.80[CHB][hapmap];0.85[JPT][hapmap]
rs1424464	0.80[CHB][hapmap]
rs1424465	0.90[CHB][hapmap];0.83[ASN][1000 genomes]
rs1424466	0.80[CHB][hapmap]
rs1424469	0.80[CHB][hapmap]
rs1557222	0.93[ASN][1000 genomes]
rs166514	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs17115685	0.88[ASN][1000 genomes]
rs17115686	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs17424216	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs17425017	1.00[JPT][hapmap]
rs17425189	0.86[JPT][hapmap]
rs17456661	0.86[JPT][hapmap]
rs17457873	0.88[ASN][1000 genomes]
rs17459384	1.00[JPT][hapmap]
rs17459948	0.86[JPT][hapmap]
rs1834151	0.80[CHB][hapmap]
rs1862925	0.90[CHB][hapmap];0.83[ASN][1000 genomes]
rs2052615	0.91[ASN][1000 genomes]
rs2052616	0.91[ASN][1000 genomes]
rs2052617	0.88[ASN][1000 genomes]
rs2113453	0.92[ASN][1000 genomes]
rs2216808	0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2405696	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2405697	0.90[CHB][hapmap];0.93[ASN][1000 genomes]
rs2405994	1.00[JPT][hapmap]
rs267638	0.86[JPT][hapmap]
rs267647	0.86[JPT][hapmap]
rs267650	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs269038	0.90[CHB][hapmap];0.93[ASN][1000 genomes]
rs269039	0.93[ASN][1000 genomes]
rs269045	0.90[CHB][hapmap]
rs2781325	0.86[JPT][hapmap]
rs3861833	0.91[CHB][hapmap];0.93[ASN][1000 genomes]
rs390203	1.00[JPT][hapmap]
rs3909556	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs3909557	0.81[ASN][1000 genomes]
rs3909558	0.93[ASN][1000 genomes]
rs4279875	0.86[JPT][hapmap]
rs439378	0.86[JPT][hapmap]
rs4912163	1.00[JPT][hapmap]
rs4912244	1.00[JPT][hapmap]
rs540431	0.90[CHB][hapmap]
rs567773	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs61769725	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6665166	0.85[ASN][1000 genomes]
rs6669975	0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6687934	0.90[CHB][hapmap];0.82[ASN][1000 genomes]
rs6690017	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs736109	0.86[JPT][hapmap]
rs736110	0.86[JPT][hapmap]
rs746937	0.86[JPT][hapmap]
rs7513076	0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7528735	0.86[ASN][1000 genomes]
rs7535763	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7540817	0.86[ASN][1000 genomes]
rs90940	0.82[CHB][hapmap]
rs9436130	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv871943	chr1:57784144-57855876	Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv871530	chr1:57793948-57858319	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv817216	chr1:57801783-58130775	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv871968	chr1:57803349-57858319	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv954	chr1:57823140-57865799	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv1001771	chr1:57837089-58068175	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57846600-57853400	Enhancers	Fetal Brain Male	brain
2	chr1:57848000-57851000	Weak transcription	Fetal Brain Female	brain
3	chr1:57848000-57851600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr1:57848000-57859800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr1:57848200-57855000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:57849200-57851800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr1:57850200-57851000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr1:57850600-57851800	Enhancers	Fetal Stomach	stomach

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