Variant report

Variant	rs101418
Chromosome Location	chr6:4083272-4083273
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:4079145..4082085-chr6:4082905..4085226,2	K562	blood:
2	chr6:4076097..4078865-chr6:4081964..4083762,3	K562	blood:
3	chr6:4076386..4078865-chr6:4079874..4083762,3	K562	blood:
4	chr6:4082801..4085618-chr6:4088964..4091515,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000252668	Chromatin interaction
ENSG00000185689	Chromatin interaction
ENSG00000145975	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs11755877	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1204951	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2326408	0.91[ASN][1000 genomes]
rs2473597	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2745453	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2745455	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2783063	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2783073	0.91[ASN][1000 genomes]
rs28878015	0.83[ASN][1000 genomes]
rs4959271	0.82[ASN][1000 genomes]
rs582008	0.80[CHB][hapmap];0.83[CHD][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs583782	0.80[CHB][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs583881	0.80[CHB][hapmap];0.83[CHD][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs584585	0.95[CHB][hapmap];0.92[CHD][hapmap];0.83[JPT][hapmap];0.91[ASN][1000 genomes]
rs588158	0.87[ASN][1000 genomes]
rs589494	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs590675	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs592953	0.93[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs593291	1.00[CHB][hapmap];0.87[CHD][hapmap];0.83[JPT][hapmap];0.92[ASN][1000 genomes]
rs594662	1.00[CHB][hapmap];0.87[CHD][hapmap];0.83[JPT][hapmap];0.93[ASN][1000 genomes]
rs595413	1.00[CHB][hapmap];0.87[CHD][hapmap];0.83[JPT][hapmap];0.93[ASN][1000 genomes]
rs608195	1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs609946	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs611500	0.91[ASN][1000 genomes]
rs612022	0.82[CHB][hapmap];0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs612477	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs613028	0.92[ASN][1000 genomes]
rs613260	0.91[ASN][1000 genomes]
rs613709	0.91[ASN][1000 genomes]
rs617604	0.99[ASN][1000 genomes]
rs617790	0.95[CHB][hapmap];0.92[CHD][hapmap];0.83[JPT][hapmap];0.91[ASN][1000 genomes]
rs619439	0.95[CHB][hapmap];0.83[JPT][hapmap];0.91[ASN][1000 genomes]
rs619483	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs619873	0.91[ASN][1000 genomes]
rs620484	0.95[CHB][hapmap];0.83[JPT][hapmap];0.91[ASN][1000 genomes]
rs620901	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs621205	0.82[ASN][1000 genomes]
rs626080	0.84[CHB][hapmap];0.92[CHD][hapmap];0.83[JPT][hapmap];0.92[ASN][1000 genomes]
rs627259	0.97[ASN][1000 genomes]
rs629362	0.95[CHB][hapmap];0.92[CHD][hapmap];0.83[JPT][hapmap];0.91[ASN][1000 genomes]
rs633290	0.95[CHB][hapmap];0.92[CHD][hapmap];0.83[JPT][hapmap];0.91[ASN][1000 genomes]
rs634114	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs634698	0.94[CHB][hapmap];0.91[ASN][1000 genomes]
rs634970	0.80[CHB][hapmap];0.83[CHD][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs638329	0.80[CHB][hapmap];0.83[CHD][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs639905	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.83[JPT][hapmap];0.81[MEX][hapmap];0.84[TSI][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs643232	0.90[CHB][hapmap];0.92[CHD][hapmap];0.83[JPT][hapmap];0.91[ASN][1000 genomes]
rs646385	0.80[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs648900	0.91[ASN][1000 genomes]
rs649725	0.95[CHB][hapmap];0.92[CHD][hapmap];0.91[ASN][1000 genomes]
rs650183	0.93[CEU][hapmap];0.81[CHB][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs651246	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs653431	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs654621	0.92[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs654982	1.00[CHB][hapmap];0.83[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs659025	1.00[CHB][hapmap];0.92[CHD][hapmap];0.83[JPT][hapmap];0.91[ASN][1000 genomes]
rs659051	0.83[ASN][1000 genomes]
rs659305	0.95[CHB][hapmap];0.92[CHD][hapmap];0.83[JPT][hapmap];0.91[ASN][1000 genomes]
rs6597028	1.00[CEU][hapmap]
rs660560	0.95[CHB][hapmap];0.92[CHD][hapmap];0.83[JPT][hapmap];0.91[ASN][1000 genomes]
rs660957	0.83[ASN][1000 genomes]
rs661404	0.95[CHB][hapmap];0.92[CHD][hapmap];0.83[JPT][hapmap];0.91[ASN][1000 genomes]
rs661657	0.99[ASN][1000 genomes]
rs662834	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs664299	0.88[ASN][1000 genomes]
rs664635	0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs664839	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs664898	0.83[ASN][1000 genomes]
rs665728	1.00[CHB][hapmap];0.87[CHD][hapmap];0.80[MEX][hapmap];0.94[ASN][1000 genomes]
rs665894	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs666254	0.93[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs668070	0.94[ASN][1000 genomes]
rs670932	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs671364	0.93[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs674543	0.96[ASN][1000 genomes]
rs676683	0.95[CHB][hapmap];0.92[CHD][hapmap];0.83[JPT][hapmap];0.91[ASN][1000 genomes]
rs678285	0.80[CHB][hapmap];0.83[CHD][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs679303	0.80[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs682063	0.93[CEU][hapmap];0.81[CHB][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs688176	0.86[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.83[JPT][hapmap];0.86[MEX][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs689308	0.91[ASN][1000 genomes]
rs694058	0.83[ASN][1000 genomes]
rs694903	0.97[ASN][1000 genomes]
rs707991	1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs7166	0.83[CHD][hapmap];0.91[ASN][1000 genomes]
rs7744628	0.95[CHB][hapmap];0.90[CHD][hapmap];0.83[JPT][hapmap];0.91[ASN][1000 genomes]
rs7756630	0.89[ASN][1000 genomes]
rs7757606	0.91[ASN][1000 genomes]
rs853416	0.95[CHB][hapmap];0.83[JPT][hapmap];0.91[ASN][1000 genomes]
rs853417	0.91[ASN][1000 genomes]
rs853418	0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs9328220	0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs9378395	0.92[ASN][1000 genomes]
rs9405219	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9405701	0.83[ASN][1000 genomes]
rs942475	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.83[JPT][hapmap];0.81[MEX][hapmap];0.84[TSI][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]

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	nsv532020	chr6:3417520-4140257	Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv1022968	chr6:3862744-4272502	Enhancers Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv538106	chr6:3862744-4272502	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv462615	chr6:4052383-4096678	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv600860	chr6:4052383-4096678	Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1030104	chr6:4062894-4240269	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs101418	PECI	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4078200-4084600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr6:4079400-4092000	Weak transcription	Right Atrium	heart
3	chr6:4082200-4084800	Weak transcription	Duodenum Mucosa	Duodenum
4	chr6:4082400-4084600	Enhancers	Brain Germinal Matrix	brain
5	chr6:4082800-4083400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr6:4083000-4083400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr6:4083000-4084000	Enhancers	Pancreas	Pancrea
8	chr6:4083200-4083400	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr6:4083200-4083400	Enhancers	iPS-18 Cell Line	embryonic stem cell

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