Variant report

Variant	rs1851104
Chromosome Location	chr2:190294549-190294550
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	chr2:190293979..190295695-chr2:190305278..190306826,2	MCF-7	breast:
2	chr2:190292778..190294660-chr2:190304417..190307256,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115368	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10166420	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10175108	1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs10188246	0.82[ASN][1000 genomes]
rs10198663	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10207812	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10210634	0.93[ASN][1000 genomes]
rs10804029	0.85[ASN][1000 genomes]
rs10931417	0.84[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs11676905	0.82[ASN][1000 genomes]
rs11677167	0.93[ASN][1000 genomes]
rs11678414	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12613903	1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs12622720	0.85[ASN][1000 genomes]
rs12623394	0.82[ASN][1000 genomes]
rs12693539	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12693540	0.85[ASN][1000 genomes]
rs12994482	0.82[ASN][1000 genomes]
rs13009912	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs13015207	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13018252	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.85[MEX][hapmap];0.92[MKK][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs13035381	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1356976	0.94[ASN][1000 genomes]
rs1520854	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.94[TSI][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1520856	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1520858	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1520866	0.87[ASN][1000 genomes]
rs1595749	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16831454	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1866605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1898971	0.85[ASN][1000 genomes]
rs1992295	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.94[TSI][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2304702	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2351932	0.81[ASN][1000 genomes]
rs2351934	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2683012	0.81[ASN][1000 genomes]
rs2882805	0.97[ASN][1000 genomes]
rs4309611	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4580411	0.90[ASN][1000 genomes]
rs4666775	0.91[ASN][1000 genomes]
rs4667280	0.91[ASN][1000 genomes]
rs4667284	0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.84[ASN][1000 genomes]
rs6434340	0.90[ASN][1000 genomes]
rs6434342	0.98[ASN][1000 genomes]
rs6434343	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.89[TSI][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6738193	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6747222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6752545	0.93[ASN][1000 genomes]
rs734859	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7420765	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7422875	0.82[ASN][1000 genomes]
rs7425383	0.82[ASN][1000 genomes]
rs744556	0.82[ASN][1000 genomes]
rs745742	0.85[ASN][1000 genomes]
rs7556928	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7566093	0.93[ASN][1000 genomes]
rs7574403	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7590098	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs8179541	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs8179732	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs893407	0.85[ASN][1000 genomes]
rs893408	0.82[ASN][1000 genomes]
rs9677436	0.87[AFR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533029	chr2:189812229-190554339	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv875613	chr2:189999011-190324685	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv875615	chr2:190215527-190444392	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv584062	chr2:190272195-190376493	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1851104	AC013439.4	cis	Muscle Skeletal	GTEx

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190286800-190294600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr2:190286800-190295000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr2:190292800-190295200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr2:190293600-190294800	Weak transcription	HepG2	liver
5	chr2:190294000-190305400	Weak transcription	Ovary	ovary

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