Variant report

Variant	rs1552839
Chromosome Location	chr12:86626227-86626228
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:86626187..86628759-chr12:86629956..86631967,2	K562	blood:

Extended variants
information (count: 145 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:136)

rs_ID	r²[population]
rs10160933	1.00[JPT][hapmap]
rs10745407	0.92[CEU][hapmap]
rs10745408	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs10776953	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10776954	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10776955	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs10776957	0.89[EUR][1000 genomes]
rs10776959	0.87[EUR][1000 genomes]
rs10776961	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs10776966	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs10776968	0.82[EUR][1000 genomes]
rs10776969	0.89[CEU][hapmap]
rs10858408	0.92[CEU][hapmap]
rs10858419	0.85[EUR][1000 genomes]
rs11103880	1.00[JPT][hapmap]
rs12309228	1.00[JPT][hapmap]
rs12311272	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12311407	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12311449	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs13378062	1.00[JPT][hapmap]
rs1389294	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1389295	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1463749	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1493408	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1493413	0.88[ASN][1000 genomes]
rs1493415	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs1493416	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1493417	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1493418	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1493419	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1493420	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1493421	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1532262	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1542780	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1602848	0.97[EUR][1000 genomes]
rs1602850	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1689340	0.92[CEU][hapmap]
rs1689357	0.93[EUR][1000 genomes]
rs1698787	0.96[CEU][hapmap];0.81[YRI][hapmap];0.93[EUR][1000 genomes]
rs1922749	0.81[CEU][hapmap]
rs1948448	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2131565	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2201281	1.00[JPT][hapmap]
rs2250915	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2405797	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2405925	0.89[CEU][hapmap]
rs2405928	0.89[CEU][hapmap]
rs2405930	0.87[EUR][1000 genomes]
rs2405933	0.83[EUR][1000 genomes]
rs2405934	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2406115	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs2406116	0.92[CEU][hapmap];0.93[YRI][hapmap];0.89[EUR][1000 genomes]
rs2406117	0.89[EUR][1000 genomes]
rs2406118	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs2406119	0.89[EUR][1000 genomes]
rs2406122	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs2406123	0.92[CEU][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2406127	0.92[CEU][hapmap]
rs2452803	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2452805	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2452806	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2452807	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs2452811	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2452815	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2465142	0.88[ASN][1000 genomes]
rs2465143	0.96[CEU][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2465144	0.96[CEU][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2465145	0.88[ASN][1000 genomes]
rs2465146	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2465147	0.82[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2465148	0.80[ASN][1000 genomes]
rs2465149	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2471560	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs2471561	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2471562	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2471563	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2471564	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2471567	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2471568	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs2471569	0.96[CEU][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2471570	0.91[EUR][1000 genomes]
rs2897278	0.80[CEU][hapmap];0.84[EUR][1000 genomes]
rs2897280	0.92[CEU][hapmap]
rs4265650	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs4329741	0.80[ASN][1000 genomes]
rs4334094	0.89[EUR][1000 genomes]
rs4503614	0.89[EUR][1000 genomes]
rs4628748	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs4842483	0.82[CEU][hapmap];0.86[EUR][1000 genomes]
rs6538025	1.00[CEU][hapmap];0.96[YRI][hapmap]
rs6538028	0.92[CEU][hapmap];0.94[YRI][hapmap]
rs6538029	0.92[CEU][hapmap]
rs6538031	0.87[EUR][1000 genomes]
rs6538032	0.87[EUR][1000 genomes]
rs6538033	0.92[CEU][hapmap]
rs7134045	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7134946	0.83[EUR][1000 genomes]
rs7135177	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs7135733	0.89[EUR][1000 genomes]
rs7135741	0.89[EUR][1000 genomes]
rs7137308	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7299319	0.88[CEU][hapmap]
rs7310186	0.87[EUR][1000 genomes]
rs7953196	0.92[CEU][hapmap]
rs7953494	0.88[ASN][1000 genomes]
rs7957560	0.92[CEU][hapmap]
rs7964553	0.92[CEU][hapmap]
rs7972484	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs7973773	0.92[CEU][hapmap]
rs839101	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs839104	0.96[CEU][hapmap]
rs839105	0.95[CEU][hapmap]
rs839137	0.81[CEU][hapmap]
rs839148	0.92[CEU][hapmap];0.83[YRI][hapmap]
rs839149	0.83[YRI][hapmap]
rs839150	0.85[YRI][hapmap]
rs839151	0.81[YRI][hapmap]
rs839153	0.84[YRI][hapmap]
rs839157	0.96[CEU][hapmap];0.83[YRI][hapmap]
rs839158	0.81[YRI][hapmap]
rs839159	0.96[CEU][hapmap];0.84[YRI][hapmap]
rs839163	0.88[EUR][1000 genomes]
rs839164	0.88[EUR][1000 genomes]
rs839165	1.00[CEU][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs839166	0.81[YRI][hapmap]
rs839168	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs839170	0.96[CEU][hapmap];0.84[YRI][hapmap]
rs839171	0.96[CEU][hapmap]
rs839191	0.87[CEU][hapmap]
rs844435	0.96[CEU][hapmap];0.83[YRI][hapmap]
rs863392	1.00[CEU][hapmap];0.97[YRI][hapmap]
rs863395	0.96[CEU][hapmap]
rs865138	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs865722	0.81[CEU][hapmap]
rs9919783	0.88[EUR][1000 genomes]
rs9919793	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049179	chr12:86056376-86799188	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	esv2761759	chr12:86415936-86747726	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv518059	chr12:86416212-86747726	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking 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
4	nsv1041397	chr12:86438607-86737558	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1053087	chr12:86569126-86733418	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv541564	chr12:86569126-86733418	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv1037003	chr12:86610040-86798121	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv1045386	chr12:86616015-86733418	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv541565	chr12:86616015-86733418	Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:86624600-86627000	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr12:86624600-86627800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr12:86625000-86627000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr12:86625400-86626400	Weak transcription	Brain Germinal Matrix	brain
5	chr12:86625400-86626400	Weak transcription	A549	lung
6	chr12:86625400-86626600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr12:86625800-86628000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr12:86626000-86628200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:86626200-86626400	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr12:86626200-86626400	Enhancers	Pancreatic Islets	Pancreatic Islet
11	chr12:86626200-86627400	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr12:86626200-86627400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr12:86626200-86627400	Enhancers	Fetal Heart	heart
14	chr12:86626200-86627400	Enhancers	HUVEC	blood vessel

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