Variant report

Variant	rs10489823
Chromosome Location	chr1:158146386-158146387
allele	A/C
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	SPI1	chr1:158146028-158146591	GM12878	blood:	n/a	n/a
2	SPI1	chr1:158146309-158146462	GM12878	blood:	n/a	n/a
3	EBF1	chr1:158146298-158146570	GM12878	blood:	n/a	n/a
4	MTA3	chr1:158146111-158146565	GM12878	blood:	n/a	n/a
5	BATF	chr1:158146178-158146468	GM12878	blood:	n/a	n/a
6	RUNX3	chr1:158146207-158146625	GM12878	blood:	n/a	n/a
7	TCF12	chr1:158146272-158146515	GM12878	blood:	n/a	n/a
8	SPI1	chr1:158146218-158146502	GM12891	blood:	n/a	n/a
9	SPI1	chr1:158146227-158146525	GM12891	blood:	n/a	n/a
10	RUNX3	chr1:158146213-158146499	GM12878	blood:	n/a	n/a
11	POU2F2	chr1:158146262-158146488	GM12891	blood:	n/a	n/a
12	SPI1	chr1:158146236-158146527	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:158137977..158140665-chr1:158145143..158147474,2	MCF-7	breast:

Variant related genes	Relation type
CD1D	TF binding region

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10489821	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12040592	0.91[CEU][hapmap]
rs12723141	0.95[JPT][hapmap]
rs1570699	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1633141	0.92[CEU][hapmap]
rs1633149	0.92[CEU][hapmap]
rs16839951	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1748383	0.92[CEU][hapmap]
rs1748387	0.92[CEU][hapmap]
rs1980757	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2269715	0.80[JPT][hapmap]
rs2518477	0.92[CEU][hapmap]
rs3021476	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3021478	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3087210	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3087211	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3087212	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3087213	0.84[EUR][1000 genomes]
rs3118165	0.92[CEU][hapmap]
rs368130	0.92[CEU][hapmap]
rs374513	0.92[CEU][hapmap]
rs377795	0.92[CEU][hapmap]
rs383688	0.92[CEU][hapmap]
rs384414	0.92[CEU][hapmap]
rs389495	0.91[CEU][hapmap]
rs393304	0.84[CEU][hapmap]
rs401904	0.92[CEU][hapmap]
rs402699	0.92[CEU][hapmap]
rs406558	0.85[CEU][hapmap]
rs407309	0.92[CEU][hapmap]
rs413557	0.92[CEU][hapmap]
rs434570	0.92[CEU][hapmap]
rs440862	0.92[CEU][hapmap]
rs448005	0.92[CEU][hapmap]
rs448556	0.92[CEU][hapmap]
rs449838	0.92[CEU][hapmap]
rs594364	0.92[CEU][hapmap]
rs607948	0.92[CEU][hapmap]
rs623215	0.92[CEU][hapmap]
rs6692064	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6692133	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs691077	0.83[CEU][hapmap]
rs691175	0.92[CEU][hapmap]
rs691551	0.92[CEU][hapmap]
rs72711995	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72711999	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7530662	0.92[CEU][hapmap];0.90[JPT][hapmap]
rs7548147	1.00[JPT][hapmap]
rs7556487	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs859001	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs859002	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs859003	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs859005	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs859008	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs859009	1.00[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs859010	1.00[CEU][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs859011	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs859013	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999542	chr1:158015715-158368132	Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv872479	chr1:158118787-158484285	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:158139400-158147400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:158143800-158149000	Weak transcription	Small Intestine	intestine
3	chr1:158145400-158147400	Enhancers	Primary B cells from peripheral blood	blood
4	chr1:158145800-158147200	Enhancers	Primary B cells from cord blood	blood
5	chr1:158146000-158147000	Bivalent Enhancer	GM12878-XiMat	blood
6	chr1:158146200-158147200	Enhancers	Primary monocytes fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links