Variant report

Variant	rs2216808
Chromosome Location	chr1:57837089-57837090
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 158 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:152)

rs_ID	r²[population]
rs10047071	0.89[ASW][hapmap];0.82[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MKK][hapmap];0.80[TSI][hapmap];0.83[YRI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10047072	0.90[ASN][1000 genomes]
rs10047073	0.89[ASW][hapmap];0.82[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.89[MKK][hapmap];0.81[TSI][hapmap];0.83[YRI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10047177	0.91[ASN][1000 genomes]
rs10047179	0.88[ASN][1000 genomes]
rs10493219	0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[ASN][1000 genomes]
rs10493221	0.80[CHB][hapmap]
rs10493225	0.86[JPT][hapmap]
rs1077424	0.82[CHB][hapmap];0.96[CHD][hapmap]
rs10889034	0.86[JPT][hapmap]
rs10889036	0.82[CHB][hapmap]
rs10889037	0.82[CHB][hapmap]
rs10889038	0.90[CHB][hapmap];1.00[CHD][hapmap]
rs10889039	0.90[CHB][hapmap];1.00[CHD][hapmap];0.85[ASN][1000 genomes]
rs10889041	0.90[CHB][hapmap];0.90[ASN][1000 genomes]
rs10889042	0.80[CHB][hapmap];0.96[CHD][hapmap]
rs10889044	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs11207010	0.85[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs11207011	0.85[CEU][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs11207012	0.82[CHB][hapmap]
rs11207016	0.90[CHB][hapmap];1.00[CHD][hapmap];0.83[ASN][1000 genomes]
rs11207018	0.85[ASN][1000 genomes]
rs11207020	0.89[ASN][1000 genomes]
rs11207021	0.91[ASN][1000 genomes]
rs11207022	0.84[ASN][1000 genomes]
rs11207026	0.80[CHB][hapmap];0.96[CHD][hapmap]
rs11207027	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs11579258	0.91[ASN][1000 genomes]
rs11581250	0.91[ASN][1000 genomes]
rs11585284	0.91[ASN][1000 genomes]
rs11585751	0.90[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs11586826	0.91[ASN][1000 genomes]
rs11590652	0.87[ASN][1000 genomes]
rs11590708	0.90[CHB][hapmap];0.83[ASN][1000 genomes]
rs11799925	0.80[CHB][hapmap]
rs12044912	0.86[JPT][hapmap]
rs12046102	0.86[JPT][hapmap]
rs12061812	0.80[CHB][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap]
rs12067263	0.90[ASN][1000 genomes]
rs12085326	0.81[ASN][1000 genomes]
rs12087888	0.85[CEU][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs12119147	0.81[CHB][hapmap];0.81[ASN][1000 genomes]
rs12119210	0.90[CHB][hapmap];1.00[CHD][hapmap];0.83[ASN][1000 genomes]
rs12124445	0.91[ASN][1000 genomes]
rs12125219	0.91[ASN][1000 genomes]
rs12126723	0.90[CHB][hapmap];0.83[ASN][1000 genomes]
rs12127603	0.91[ASN][1000 genomes]
rs12128305	0.86[JPT][hapmap]
rs12132685	0.86[JPT][hapmap]
rs12136107	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12137169	0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap]
rs12137540	0.85[ASN][1000 genomes]
rs12139429	0.80[CHB][hapmap];0.96[CHD][hapmap]
rs12142821	0.80[CHB][hapmap];0.86[JPT][hapmap]
rs12240237	0.90[CHB][hapmap];0.83[ASN][1000 genomes]
rs1240442	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1240443	0.90[ASN][1000 genomes]
rs12405761	0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12565446	0.90[CHB][hapmap];0.83[ASN][1000 genomes]
rs12565636	0.83[ASN][1000 genomes]
rs12566690	0.89[ASN][1000 genomes]
rs12568449	0.85[JPT][hapmap]
rs12726704	1.00[JPT][hapmap]
rs12741210	0.82[CHB][hapmap]
rs12752978	0.86[JPT][hapmap]
rs1334239	0.86[JPT][hapmap]
rs1334240	0.86[JPT][hapmap]
rs1364444	0.83[ASN][1000 genomes]
rs1424462	0.90[CHB][hapmap];0.83[ASN][1000 genomes]
rs1424463	0.90[CHB][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs1424464	0.90[CHB][hapmap];0.83[ASN][1000 genomes]
rs1424465	0.82[CHB][hapmap];1.00[CHD][hapmap]
rs1424466	0.90[CHB][hapmap]
rs1424467	0.90[CHB][hapmap];1.00[CHD][hapmap];0.83[ASN][1000 genomes]
rs1424468	0.83[ASN][1000 genomes]
rs1424469	0.90[CHB][hapmap];0.83[ASN][1000 genomes]
rs1424470	0.83[ASN][1000 genomes]
rs1504594	0.82[CHB][hapmap]
rs1557222	0.90[ASN][1000 genomes]
rs166514	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs17115685	0.91[ASN][1000 genomes]
rs17115686	0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[ASN][1000 genomes]
rs17115750	0.80[CHB][hapmap]
rs17423255	0.90[CHB][hapmap];1.00[CHD][hapmap];0.83[ASN][1000 genomes]
rs17424216	0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs17425017	0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs17425189	0.86[JPT][hapmap]
rs17456661	0.80[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap]
rs17457873	0.91[ASN][1000 genomes]
rs17458730	0.80[CHB][hapmap]
rs17459384	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs17459948	0.86[JPT][hapmap]
rs1834151	0.90[CHB][hapmap];0.83[ASN][1000 genomes]
rs1862925	0.82[CHB][hapmap];1.00[CHD][hapmap]
rs2052615	0.87[ASN][1000 genomes]
rs2052616	0.87[ASN][1000 genomes]
rs2052617	0.91[ASN][1000 genomes]
rs2113453	0.88[ASN][1000 genomes]
rs2405696	0.82[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2405697	0.82[CHB][hapmap];1.00[CHD][hapmap];0.90[ASN][1000 genomes]
rs2405994	0.90[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs267638	0.92[CHD][hapmap];0.86[JPT][hapmap]
rs267647	0.92[CHD][hapmap];0.86[JPT][hapmap]
rs267650	0.85[CEU][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs267651	0.92[CHD][hapmap]
rs269038	0.82[CHB][hapmap];1.00[CHD][hapmap];0.90[ASN][1000 genomes]
rs269039	0.90[ASN][1000 genomes]
rs269045	0.82[CHB][hapmap];0.96[CHD][hapmap]
rs269048	0.80[CHB][hapmap]
rs269049	0.80[CHB][hapmap];0.96[CHD][hapmap]
rs2781325	0.86[JPT][hapmap]
rs3738553	0.80[CHB][hapmap]
rs3844041	0.85[CHD][hapmap]
rs3850549	0.80[CHB][hapmap];0.96[CHD][hapmap]
rs3850552	0.80[CHB][hapmap];0.92[CHD][hapmap]
rs3850556	0.88[CHD][hapmap]
rs3861833	0.82[CHB][hapmap];0.90[ASN][1000 genomes]
rs3861834	0.80[CHB][hapmap];0.92[CHD][hapmap]
rs3896279	0.80[CHB][hapmap];0.96[CHD][hapmap]
rs390203	1.00[JPT][hapmap]
rs3909556	0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[ASN][1000 genomes]
rs3909557	0.84[ASN][1000 genomes]
rs3909558	0.90[ASN][1000 genomes]
rs4279875	0.86[JPT][hapmap]
rs439378	0.92[CHD][hapmap];0.86[JPT][hapmap]
rs4912163	0.80[CHB][hapmap];1.00[JPT][hapmap]
rs4912244	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs532926	0.80[CHB][hapmap];0.96[CHD][hapmap]
rs540431	0.82[CHB][hapmap];0.96[CHD][hapmap]
rs563099	0.80[CHB][hapmap];0.96[CHD][hapmap]
rs563270	0.80[CHB][hapmap];0.95[CHD][hapmap]
rs564951	0.86[CHB][hapmap]
rs565032	0.80[CHB][hapmap]
rs566847	0.80[CHB][hapmap];0.92[CHD][hapmap]
rs567773	0.82[CHB][hapmap];1.00[CHD][hapmap];0.82[ASN][1000 genomes]
rs61769725	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587767	0.92[CHD][hapmap]
rs6665166	0.82[ASN][1000 genomes]
rs6669975	1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6677561	0.83[ASN][1000 genomes]
rs6687842	0.80[CHB][hapmap];0.96[CHD][hapmap]
rs6687934	0.82[CHB][hapmap];1.00[CHD][hapmap];0.81[ASN][1000 genomes]
rs6690017	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs736109	0.92[CHD][hapmap];0.86[JPT][hapmap]
rs736110	0.86[JPT][hapmap]
rs746937	0.92[CHD][hapmap];0.86[JPT][hapmap]
rs7513076	0.80[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7528735	0.89[CHB][hapmap];0.89[ASN][1000 genomes]
rs7535763	0.89[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.89[MKK][hapmap];0.83[TSI][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7540817	0.89[ASN][1000 genomes]
rs90940	0.96[CHD][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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2216808	DAB1	cis	cerebellum	SCAN
rs2216808	YIPF1	cis	parietal	SCAN
rs2216808	C1orf168	cis	cerebellum	SCAN
rs2216808	DIO1	cis	parietal	SCAN
rs2216808	PARS2	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57829600-57843400	Weak transcription	Fetal Heart	heart
2	chr1:57830200-57841800	Weak transcription	Fetal Brain Male	brain
3	chr1:57834800-57843200	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr1:57835000-57843200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr1:57835600-57837200	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr1:57835600-57837200	Enhancers	iPS-20b Cell Line	embryonic stem cell
7	chr1:57835800-57843000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:57836800-57837400	Enhancers	H9 Cell Line	embryonic stem cell
9	chr1:57837000-57837400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr1:57837000-57839800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr1:57837000-57843200	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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