Variant report

Variant	rs12021915
Chromosome Location	chr1:171714296-171714297
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:171714070-171714489	U87	brain:	n/a	n/a
2	FOS	chr1:171714186-171714454	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr1:171713950-171714489	U87	brain:	n/a	n/a
4	GATA3	chr1:171714281-171714491	SH-SY5Y	brain:	n/a	n/a
5	STAT3	chr1:171714168-171714483	MCF10A-Er-Src	breast:	n/a	n/a
6	E2F4	chr1:171714175-171714354	MCF10A-Er-Src	breast:	n/a	n/a
7	STAT3	chr1:171714153-171714536	MCF10A-Er-Src	breast:	n/a	n/a
8	FOS	chr1:171714147-171714989	MCF10A-Er-Src	breast:	n/a	chr1:171714858-171714869
9	FOS	chr1:171714120-171714540	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr1:171713530-171715114	K562	blood:	n/a	n/a
11	STAT3	chr1:171714224-171714423	MCF10A-Er-Src	breast:	n/a	n/a
12	STAT3	chr1:171714161-171714475	MCF10A-Er-Src	breast:	n/a	n/a
13	FOS	chr1:171714197-171714516	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:171710341..171715416-chr1:171748571..171752440,7	MCF-7	breast:
2	chr1:171709915..171712765-chr1:171713843..171716180,3	MCF-7	breast:
3	chr1:171709343..171715185-chr1:171748592..171756289,15	K562	blood:
4	chr1:171710254..171714548-chr1:171728803..171733052,4	K562	blood:
5	chr1:171709981..171712025-chr1:171713091..171714877,2	K562	blood:
6	chr1:171712949..171715185-chr1:171753608..171756289,2	K562	blood:
7	chr1:171710037..171714996-chr1:171734843..171738629,6	MCF-7	breast:

No data

Variant related genes	Relation type
VAMP4	TF binding region
ENSG00000236741	Chromatin interaction
ENSG00000253060	Chromatin interaction
ENSG00000010165	Chromatin interaction
ENSG00000117533	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10489250	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12022661	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12024194	1.00[CEU][hapmap];0.89[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12024335	0.85[EUR][1000 genomes]
rs12028096	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12029218	0.83[AFR][1000 genomes]
rs12034114	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12035719	0.83[CEU][hapmap]
rs12036980	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12089083	0.95[ASN][1000 genomes]
rs1490185	0.83[CEU][hapmap]
rs16843227	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2421910	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57300412	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58081399	0.92[ASN][1000 genomes]
rs61413126	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6659266	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6665590	0.92[ASN][1000 genomes]
rs6665614	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72717888	0.83[AFR][1000 genomes]
rs72717895	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72717900	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72719512	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7543786	1.00[CEU][hapmap]
rs7554793	1.00[CHB][hapmap];1.00[JPT][hapmap];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	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv3512995	chr1:171329123-171994470	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	esv3512997	chr1:171329123-171994470	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	esv12447	chr1:171556291-171726822	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171712000-171723400	Weak transcription	Lung	lung
2	chr1:171712200-171715800	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr1:171712400-171714600	Weak transcription	Primary B cells from cord blood	blood
4	chr1:171713000-171714400	Enhancers	Skeletal Muscle Female	skeletal muscle
5	chr1:171713200-171714400	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr1:171713400-171716200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr1:171713600-171722200	Weak transcription	NHLF	lung
8	chr1:171713600-171722800	Weak transcription	HMEC	breast
9	chr1:171714000-171714600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
10	chr1:171714000-171714800	Enhancers	Primary neutrophils fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links