Variant report

Variant	rs1858480
Chromosome Location	chr1:152301735-152301736
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr1:152301102-152301801	SK-N-SH	brain:	n/a	chr1:152301454-152301461 chr1:152301450-152301466 chr1:152301453-152301463 chr1:152301306-152301316 chr1:152301453-152301461 chr1:152301454-152301461 chr1:152301454-152301461 chr1:152301454-152301463
2	GATA3	chr1:152301211-152301782	SK-N-SH	brain:	n/a	chr1:152301454-152301461 chr1:152301450-152301466 chr1:152301453-152301463 chr1:152301306-152301316 chr1:152301453-152301461 chr1:152301454-152301461 chr1:152301454-152301461 chr1:152301454-152301463

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:152297812..152299892-chr1:152301033..152302777,2	MCF-7	breast:

Variant related genes	Relation type
FLG	TF binding region

Extended variants
information (count: 117 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs10749669	1.00[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap]
rs10749670	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10788824	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap]
rs10788831	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10888470	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap]
rs10888471	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap]
rs10888473	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap]
rs10888476	0.85[ASN][1000 genomes]
rs10888477	0.87[ASN][1000 genomes]
rs10888478	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11204947	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap]
rs11204948	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap]
rs11204949	0.91[CHB][hapmap];0.80[CHD][hapmap];0.82[GIH][hapmap]
rs11204956	0.84[ASN][1000 genomes]
rs11204976	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11204978	0.91[CEU][hapmap];0.91[CHB][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11204980	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11204981	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11485508	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11576858	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11581433	0.81[EUR][1000 genomes]
rs11583524	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap]
rs11584340	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11584427	0.92[CEU][hapmap];0.91[CHB][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11586114	0.93[CEU][hapmap];0.91[CHB][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11587676	0.93[CEU][hapmap]
rs11588170	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11588174	1.00[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap]
rs12027807	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12027899	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12045492	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12045496	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12065368	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12405278	0.91[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.81[MEX][hapmap];0.81[EUR][1000 genomes]
rs12407156	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12407553	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12407807	0.81[EUR][1000 genomes]
rs12409802	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12730241	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1390488	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap]
rs1390490	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap]
rs1496045	1.00[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap]
rs1858479	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1858482	1.00[ASW][hapmap];0.93[CEU][hapmap];0.91[CHB][hapmap];0.86[GIH][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2065955	0.93[CEU][hapmap];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2065956	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2184950	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2184951	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2184953	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2184954	0.81[EUR][1000 genomes]
rs2338555	0.92[CEU][hapmap];0.88[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2338556	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3091276	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3120642	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3120653	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3120659	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3120661	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3120662	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3126054	0.85[EUR][1000 genomes]
rs3126055	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3126056	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3126058	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3126060	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3126062	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3126066	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.83[YRI][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3126067	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3126072	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3126074	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3126079	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3126085	1.00[ASW][hapmap];0.86[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];0.91[LWK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3126088	1.00[ASW][hapmap];0.93[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3126089	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3126090	0.87[ASW][hapmap];0.82[YRI][hapmap]
rs3126091	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3126092	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3126093	0.83[YRI][hapmap]
rs3126094	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3126095	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3126097	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3126098	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34029395	0.82[ASN][1000 genomes]
rs34188926	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41267154	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4256811	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4341364	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4361987	0.83[ASN][1000 genomes]
rs4456097	0.81[ASN][1000 genomes]
rs4466659	0.86[ASN][1000 genomes]
rs4845423	1.00[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap]
rs4845736	1.00[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap]
rs4845737	0.91[JPT][hapmap]
rs4845745	1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap]
rs4845750	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap]
rs4845753	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55650366	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57672167	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6587666	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6666382	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap]
rs6681433	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6681457	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66831674	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6692010	0.80[ASN][1000 genomes]
rs71625201	0.95[EUR][1000 genomes]
rs71625202	0.91[EUR][1000 genomes]
rs72697000	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72698906	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs74129461	0.97[EUR][1000 genomes]
rs7540844	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7543541	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7550106	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap]
rs877776	1.00[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap]
rs9435974	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9436062	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[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	nsv1014095	chr1:152104486-152454591	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv1005472	chr1:152247763-152443448	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv535161	chr1:152247763-152443448	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv998298	chr1:152288685-152319877	Enhancers Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1858480	JTB	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:152286600-152322200	Weak transcription	Ovary	ovary
2	chr1:152300000-152303800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr1:152300400-152302000	Enhancers	HSMM	muscle
4	chr1:152301000-152301800	Enhancers	HSMMtube	muscle
5	chr1:152301000-152302200	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr1:152301000-152302200	Enhancers	HMEC	breast
7	chr1:152301200-152302000	Enhancers	NHEK	skin
8	chr1:152301200-152302400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr1:152301400-152301800	Enhancers	Placenta Amnion	Placenta Amnion
10	chr1:152301600-152301800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr1:152301600-152302000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links