Variant report

Variant	rs3087212
Chromosome Location	chr1:158146273-158146274
allele	C/T
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	MTA3	chr1:158146111-158146565	GM12878	blood:	n/a	n/a
3	BATF	chr1:158146178-158146468	GM12878	blood:	n/a	n/a
4	RUNX3	chr1:158146207-158146625	GM12878	blood:	n/a	n/a
5	TCF12	chr1:158146272-158146515	GM12878	blood:	n/a	n/a
6	SPI1	chr1:158146218-158146502	GM12891	blood:	n/a	n/a
7	SPI1	chr1:158146227-158146525	GM12891	blood:	n/a	n/a
8	RUNX3	chr1:158146213-158146499	GM12878	blood:	n/a	n/a
9	POU2F2	chr1:158146262-158146488	GM12891	blood:	n/a	n/a
10	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: 58 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10489821	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10489823	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]
rs12040592	0.91[CEU][hapmap]
rs12723141	0.95[JPT][hapmap]
rs1570699	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];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	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2518477	0.92[CEU][hapmap]
rs3021476	1.00[AFR][1000 genomes];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[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];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[YRI][hapmap];1.00[AFR][1000 genomes];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]
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	0.81[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];0.88[MEX][hapmap]
rs7548147	1.00[JPT][hapmap]
rs7556487	0.98[AFR][1000 genomes];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	0.82[AFR][1000 genomes];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[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs859009	1.00[CEU][hapmap];0.95[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];1.00[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.94[TSI][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];0.98[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3087212	SHE	cis	cerebellum	SCAN
rs3087212	NCSTN	cis	cerebellum	SCAN
rs3087212	IQGAP3	cis	cerebellum	SCAN
rs3087212	CD1A	cis	cerebellum	SCAN
rs3087212	LCE1E	cis	parietal	SCAN
rs3087212	VHLL	cis	parietal	SCAN

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

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