Variant report

Variant	rs12087888
Chromosome Location	chr1:57802759-57802760
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:57797489..57800179-chr1:57802405..57805312,2	K562	blood:

Extended variants
information (count: 150 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:145)

rs_ID	r²[population]
rs10047071	0.81[CHB][hapmap];0.96[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs10047073	0.81[CHB][hapmap];0.96[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs10493219	0.81[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap]
rs10493225	1.00[JPT][hapmap]
rs1077424	0.91[CHB][hapmap];1.00[CHD][hapmap];0.93[ASN][1000 genomes]
rs1077425	0.93[ASN][1000 genomes]
rs10889034	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10889035	0.90[ASN][1000 genomes]
rs10889036	0.91[CHB][hapmap];0.93[ASN][1000 genomes]
rs10889037	0.85[ASN][1000 genomes]
rs10889038	0.81[CHB][hapmap];0.96[CHD][hapmap]
rs10889039	0.81[CHB][hapmap];0.96[CHD][hapmap];0.86[ASN][1000 genomes]
rs10889041	0.81[CHB][hapmap]
rs10889042	0.92[CHD][hapmap]
rs10889044	0.86[JPT][hapmap]
rs11207007	0.81[CHB][hapmap];0.83[ASN][1000 genomes]
rs11207010	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.88[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11207011	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11207012	0.91[CHB][hapmap];0.93[ASN][1000 genomes]
rs11207013	0.90[ASN][1000 genomes]
rs11207014	0.93[ASN][1000 genomes]
rs11207015	0.93[ASN][1000 genomes]
rs11207016	0.81[CHB][hapmap];0.96[CHD][hapmap];0.88[ASN][1000 genomes]
rs11207017	0.85[ASN][1000 genomes]
rs11207018	0.86[ASN][1000 genomes]
rs11207026	0.92[CHD][hapmap]
rs1149630	0.86[ASN][1000 genomes]
rs11585751	0.81[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap]
rs11588755	0.83[ASN][1000 genomes]
rs11589921	0.84[ASN][1000 genomes]
rs11590708	0.81[CHB][hapmap];0.88[ASN][1000 genomes]
rs12044912	1.00[JPT][hapmap]
rs12046102	1.00[JPT][hapmap]
rs12061812	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12085326	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12119147	0.86[ASN][1000 genomes]
rs12119210	0.81[CHB][hapmap];0.96[CHD][hapmap];0.88[ASN][1000 genomes]
rs12126723	0.81[CHB][hapmap];0.88[ASN][1000 genomes]
rs12128305	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12132685	1.00[JPT][hapmap]
rs12136107	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs12137169	0.81[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap]
rs12137583	0.91[ASN][1000 genomes]
rs12139429	0.92[CHD][hapmap]
rs12142821	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12240237	0.81[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs1240439	0.90[ASN][1000 genomes]
rs1240442	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs12405761	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs12565446	0.81[CHB][hapmap];0.88[ASN][1000 genomes]
rs12565636	0.88[ASN][1000 genomes]
rs12568449	1.00[JPT][hapmap]
rs12726704	1.00[JPT][hapmap]
rs12741210	0.85[ASN][1000 genomes]
rs12752978	1.00[JPT][hapmap]
rs1334239	1.00[JPT][hapmap]
rs1334240	1.00[JPT][hapmap]
rs1364444	0.88[ASN][1000 genomes]
rs1424462	0.88[ASN][1000 genomes]
rs1424463	0.81[CHB][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs1424464	0.81[CHB][hapmap];0.88[ASN][1000 genomes]
rs1424465	0.96[CHD][hapmap];0.85[ASN][1000 genomes]
rs1424466	0.81[CHB][hapmap]
rs1424467	0.81[CHB][hapmap];0.96[CHD][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs1424468	0.88[ASN][1000 genomes]
rs1424469	0.81[CHB][hapmap];0.88[ASN][1000 genomes]
rs1424470	0.88[ASN][1000 genomes]
rs1504594	0.91[CHB][hapmap];0.93[ASN][1000 genomes]
rs166514	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs17115686	0.81[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap]
rs17423255	0.81[CHB][hapmap];0.96[CHD][hapmap];0.88[ASN][1000 genomes]
rs17424216	0.81[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap]
rs17425017	0.81[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap]
rs17425189	1.00[JPT][hapmap]
rs17456661	0.90[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs17459384	0.86[JPT][hapmap]
rs17459948	1.00[JPT][hapmap]
rs1809976	0.90[ASN][1000 genomes]
rs1834151	0.81[CHB][hapmap];0.88[ASN][1000 genomes]
rs1862925	0.96[CHD][hapmap];0.85[ASN][1000 genomes]
rs2113456	0.93[ASN][1000 genomes]
rs2161808	0.90[ASN][1000 genomes]
rs2216808	0.85[CEU][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs2405696	0.81[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs2405697	0.96[CHD][hapmap]
rs2405994	0.81[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap]
rs267638	0.89[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs267646	0.90[ASN][1000 genomes]
rs267647	0.81[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs267650	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs267651	0.96[CHD][hapmap];0.81[ASN][1000 genomes]
rs269038	0.96[CHD][hapmap]
rs269045	0.92[CHD][hapmap]
rs269049	0.92[CHD][hapmap]
rs2781325	1.00[JPT][hapmap]
rs28706213	0.86[ASN][1000 genomes]
rs35804651	0.90[ASN][1000 genomes]
rs374845	0.86[ASN][1000 genomes]
rs3844041	0.81[CHD][hapmap]
rs3850549	0.92[CHD][hapmap]
rs3850552	0.89[CHD][hapmap]
rs3850556	0.85[CHD][hapmap]
rs3861834	0.89[CHD][hapmap]
rs3896279	0.92[CHD][hapmap]
rs390203	0.81[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3909556	0.81[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap]
rs4279875	1.00[JPT][hapmap]
rs439378	0.89[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4912162	0.91[ASN][1000 genomes]
rs4912163	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4912237	0.91[ASN][1000 genomes]
rs4912244	0.88[CHB][hapmap];0.86[JPT][hapmap]
rs532926	0.92[CHD][hapmap]
rs540431	0.92[CHD][hapmap]
rs55863020	0.91[ASN][1000 genomes]
rs563099	0.92[CHD][hapmap]
rs563270	0.91[CHD][hapmap]
rs566847	0.89[CHD][hapmap]
rs567773	0.96[CHD][hapmap]
rs61769668	0.93[ASN][1000 genomes]
rs61769725	0.84[ASN][1000 genomes]
rs6587767	0.96[CHD][hapmap];0.81[ASN][1000 genomes]
rs6665166	0.83[ASN][1000 genomes]
rs6668257	0.83[ASN][1000 genomes]
rs6669975	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6677561	0.88[ASN][1000 genomes]
rs6687842	0.92[CHD][hapmap]
rs6687934	0.96[CHD][hapmap];0.86[ASN][1000 genomes]
rs6690017	0.83[ASN][1000 genomes]
rs72674872	0.81[ASN][1000 genomes]
rs736109	0.89[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs736110	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs746937	0.89[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7513076	0.86[JPT][hapmap]
rs7535763	0.90[CHB][hapmap];0.96[CHD][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs7543805	0.93[ASN][1000 genomes]
rs7547412	0.85[ASN][1000 genomes]
rs7547509	0.90[ASN][1000 genomes]
rs77510	0.90[ASN][1000 genomes]
rs77511	0.90[ASN][1000 genomes]
rs882283	0.90[ASN][1000 genomes]
rs90940	0.83[CHB][hapmap];1.00[CHD][hapmap];0.90[ASN][1000 genomes]
rs924848	0.83[ASN][1000 genomes]
rs94216	0.86[ASN][1000 genomes]
rs9436130	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12087888	C1orf168	cis	cerebellum	SCAN
rs12087888	YIPF1	cis	parietal	SCAN
rs12087888	PARS2	cis	cerebellum	SCAN
rs12087888	DAB1	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57792400-57806200	Weak transcription	Fetal Intestine Small	intestine
2	chr1:57800000-57826600	Weak transcription	Left Ventricle	heart
3	chr1:57801200-57803200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr1:57801600-57803800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr1:57801800-57803200	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr1:57802000-57803200	Enhancers	iPS-20b Cell Line	embryonic stem cell
7	chr1:57802000-57803800	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr1:57802200-57803000	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr1:57802200-57803200	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr1:57802200-57803400	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr1:57802200-57803400	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr1:57802200-57809000	Weak transcription	Fetal Brain Male	brain
13	chr1:57802400-57806200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr1:57802600-57803200	Enhancers	H1 Cell Line	embryonic stem cell
15	chr1:57802600-57803200	Enhancers	H9 Cell Line	embryonic stem cell
16	chr1:57802600-57803200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell

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