Variant report

Variant	rs12022859
Chromosome Location	chr1:94810285-94810286
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	chr1:94485354..94487209-chr1:94808171..94810655,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198691	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1054626	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11165103	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11165114	0.95[EUR][1000 genomes]
rs12024941	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12026367	0.85[ASN][1000 genomes]
rs12027548	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12031606	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12036085	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12038745	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12039546	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12042509	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs12046536	1.00[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap];0.92[EUR][1000 genomes]
rs12093742	0.90[EUR][1000 genomes]
rs12562103	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12563826	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1360365	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1572575	0.85[ASN][1000 genomes]
rs1576592	0.91[EUR][1000 genomes]
rs1611832	0.94[EUR][1000 genomes]
rs1622451	0.97[EUR][1000 genomes]
rs1623248	0.97[EUR][1000 genomes]
rs1623314	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[EUR][1000 genomes]
rs1629275	0.94[EUR][1000 genomes]
rs1687947	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[CHD][hapmap];0.82[JPT][hapmap];0.83[TSI][hapmap];0.91[EUR][1000 genomes]
rs1687950	0.93[EUR][1000 genomes]
rs16928	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];0.94[TSI][hapmap];0.95[EUR][1000 genomes]
rs17111408	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17111419	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17111426	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.90[MKK][hapmap];0.94[TSI][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17111436	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1765636	0.97[EUR][1000 genomes]
rs1765640	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes]
rs1929131	0.86[CEU][hapmap];0.89[CHB][hapmap];0.82[EUR][1000 genomes]
rs1999270	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.83[TSI][hapmap];0.91[EUR][1000 genomes]
rs1999271	1.00[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap];0.91[EUR][1000 genomes]
rs2130899	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2391472	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35275815	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3789690	0.83[EUR][1000 genomes]
rs4543802	1.00[EUR][1000 genomes]
rs4847201	1.00[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap];0.91[EUR][1000 genomes]
rs4847296	0.90[EUR][1000 genomes]
rs55961421	0.92[EUR][1000 genomes]
rs56037795	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57666908	0.83[EUR][1000 genomes]
rs6541343	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.83[TSI][hapmap];0.91[EUR][1000 genomes]
rs6541345	0.91[EUR][1000 genomes]
rs6662877	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6673491	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.83[TSI][hapmap];0.90[EUR][1000 genomes]
rs6675959	1.00[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap];0.91[EUR][1000 genomes]
rs6681827	1.00[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap];0.91[EUR][1000 genomes]
rs66918029	0.92[EUR][1000 genomes]
rs66961454	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs67180557	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67554381	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs67612304	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67681803	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs67807923	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs68193246	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7413345	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7415246	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7515965	0.91[EUR][1000 genomes]
rs7520754	0.90[EUR][1000 genomes]
rs7525320	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7533977	0.91[EUR][1000 genomes]
rs7554714	1.00[CEU][hapmap];0.88[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap];0.91[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428510	chr1:94709575-94866655	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94799200-94812000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:94805600-94810400	Weak transcription	Stomach Mucosa	stomach
3	chr1:94806400-94814600	Weak transcription	Thymus	Thymus
4	chr1:94807800-94811000	Enhancers	Placenta	Placenta
5	chr1:94808200-94814400	Weak transcription	Fetal Thymus	thymus
6	chr1:94808800-94810800	Weak transcription	Fetal Intestine Large	intestine
7	chr1:94810000-94810400	Enhancers	Placenta Amnion	Placenta Amnion
8	chr1:94810000-94810800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr1:94810000-94811800	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr1:94810200-94810400	Enhancers	Monocytes-CD14+_RO01746	blood
11	chr1:94810200-94811000	Enhancers	HepG2	liver
12	chr1:94810200-94811400	Enhancers	Primary neutrophils fromperipheralblood	blood

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