Variant report

Variant	rs12142821
Chromosome Location	chr1:57806895-57806896
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 139 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:133)

rs_ID	r²[population]
rs10047071	0.86[JPT][hapmap]
rs10047073	0.86[JPT][hapmap]
rs10493219	0.83[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs10493221	0.80[CHB][hapmap]
rs10493225	1.00[JPT][hapmap]
rs1077424	0.82[CHB][hapmap];0.85[ASN][1000 genomes]
rs1077425	0.85[ASN][1000 genomes]
rs10889034	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10889035	0.82[ASN][1000 genomes]
rs10889036	0.82[CHB][hapmap];0.85[ASN][1000 genomes]
rs10889042	0.80[CHB][hapmap]
rs10889044	0.89[CHB][hapmap];0.86[JPT][hapmap]
rs11207007	0.90[CHB][hapmap];0.91[ASN][1000 genomes]
rs11207010	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11207011	0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11207012	0.82[CHB][hapmap];0.85[ASN][1000 genomes]
rs11207013	0.82[ASN][1000 genomes]
rs11207014	0.85[ASN][1000 genomes]
rs11207015	0.85[ASN][1000 genomes]
rs11207020	0.85[ASN][1000 genomes]
rs11207021	0.83[ASN][1000 genomes]
rs11207026	0.80[CHB][hapmap]
rs11207027	0.82[CHB][hapmap]
rs11579258	0.83[ASN][1000 genomes]
rs11581250	0.83[ASN][1000 genomes]
rs11585284	0.83[ASN][1000 genomes]
rs11585751	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs11586826	0.83[ASN][1000 genomes]
rs11589921	0.93[ASN][1000 genomes]
rs11799925	0.80[CHB][hapmap];0.87[ASN][1000 genomes]
rs12044912	1.00[JPT][hapmap]
rs12046102	1.00[JPT][hapmap]
rs12061812	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12085326	0.88[ASN][1000 genomes]
rs12087888	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12124445	0.83[ASN][1000 genomes]
rs12125219	0.83[ASN][1000 genomes]
rs12127603	0.83[ASN][1000 genomes]
rs12128305	0.96[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12132685	1.00[JPT][hapmap]
rs12136107	0.84[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs12137169	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs12137540	0.82[ASN][1000 genomes]
rs12137583	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12139429	0.80[CHB][hapmap];0.87[ASN][1000 genomes]
rs12240237	0.86[JPT][hapmap]
rs1240439	0.81[ASN][1000 genomes]
rs1240442	0.80[CHB][hapmap];0.86[JPT][hapmap]
rs12405761	0.86[JPT][hapmap]
rs12566690	0.85[ASN][1000 genomes]
rs12568449	1.00[JPT][hapmap]
rs12726704	1.00[JPT][hapmap]
rs12752978	1.00[JPT][hapmap]
rs1334239	1.00[JPT][hapmap]
rs1334240	1.00[JPT][hapmap]
rs1424463	0.85[JPT][hapmap]
rs1424467	0.85[JPT][hapmap]
rs1504594	0.82[CHB][hapmap];0.85[ASN][1000 genomes]
rs166514	0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs17115685	0.83[ASN][1000 genomes]
rs17115686	0.83[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs17115750	0.80[CHB][hapmap]
rs17424216	0.83[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs17425017	0.90[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs17425189	1.00[JPT][hapmap]
rs17456661	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17457873	0.83[ASN][1000 genomes]
rs17458730	0.80[CHB][hapmap]
rs17459384	0.89[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs17459948	1.00[JPT][hapmap]
rs1809976	0.82[ASN][1000 genomes]
rs2052617	0.83[ASN][1000 genomes]
rs2113454	0.87[ASN][1000 genomes]
rs2113456	0.85[ASN][1000 genomes]
rs2161808	0.82[ASN][1000 genomes]
rs2216808	0.80[CHB][hapmap];0.86[JPT][hapmap]
rs2405696	0.86[JPT][hapmap]
rs2405994	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs267638	1.00[JPT][hapmap]
rs267646	0.81[ASN][1000 genomes]
rs267647	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs267650	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs267651	0.82[CHB][hapmap];0.90[ASN][1000 genomes]
rs269044	0.80[CHB][hapmap]
rs269048	0.80[CHB][hapmap]
rs269049	0.80[CHB][hapmap]
rs269050	0.80[CHB][hapmap]
rs269057	0.80[CHB][hapmap]
rs2781325	1.00[JPT][hapmap]
rs28706213	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35804651	0.82[ASN][1000 genomes]
rs3738553	0.80[CHB][hapmap]
rs3850549	0.80[CHB][hapmap]
rs3850552	0.80[CHB][hapmap]
rs3861834	0.80[CHB][hapmap]
rs3896279	0.80[CHB][hapmap]
rs390203	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs3909556	0.83[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs4279875	1.00[JPT][hapmap]
rs439378	1.00[JPT][hapmap]
rs4912162	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4912163	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4912237	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4912244	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs532926	0.80[CHB][hapmap]
rs55863020	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs563099	0.80[CHB][hapmap]
rs563270	0.80[CHB][hapmap]
rs564951	0.86[CHB][hapmap]
rs565032	0.80[CHB][hapmap]
rs566847	0.80[CHB][hapmap]
rs61769668	0.85[ASN][1000 genomes]
rs61769670	0.87[ASN][1000 genomes]
rs6587767	0.82[CHB][hapmap];0.90[ASN][1000 genomes]
rs6668257	0.91[ASN][1000 genomes]
rs6669975	1.00[JPT][hapmap]
rs6687842	0.80[CHB][hapmap];0.87[ASN][1000 genomes]
rs72674872	0.89[ASN][1000 genomes]
rs736109	1.00[JPT][hapmap]
rs736110	1.00[JPT][hapmap]
rs746937	1.00[JPT][hapmap]
rs7513076	0.80[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs7528735	0.89[CHB][hapmap];0.85[ASN][1000 genomes]
rs7535763	0.86[JPT][hapmap]
rs7540817	0.85[ASN][1000 genomes]
rs7543805	0.85[ASN][1000 genomes]
rs7547509	0.82[ASN][1000 genomes]
rs77510	0.82[ASN][1000 genomes]
rs77511	0.82[ASN][1000 genomes]
rs882283	0.82[ASN][1000 genomes]
rs90940	0.82[ASN][1000 genomes]
rs924848	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9436130	1.00[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	nsv461628	chr1:57463326-57816489	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv546305	chr1:57463326-57816489	Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57800000-57826600	Weak transcription	Left Ventricle	heart
2	chr1:57802200-57809000	Weak transcription	Fetal Brain Male	brain
3	chr1:57803200-57816000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr1:57803800-57811600	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr1:57805200-57807200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr1:57806000-57807400	Weak transcription	Fetal Brain Female	brain
7	chr1:57806200-57807600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr1:57806800-57810400	Weak transcription	Fetal Heart	heart
9	chr1:57806800-57810800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links