Variant report

Variant	rs2987983
Chromosome Location	chr14:64763653-64763654
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	GATA2	chr14:64763309-64763702	HUVEC	blood vessel:	n/a	chr14:64763527-64763537
2	FOS	chr14:64763233-64763797	HUVEC	blood vessel:	n/a	chr14:64763574-64763582 chr14:64763575-64763586 chr14:64763572-64763584 chr14:64763567-64763579 chr14:64763572-64763583
3	BATF	chr14:64763391-64763672	GM12878	blood:	n/a	n/a
4	FOS	chr14:64763436-64763728	MCF10A-Er-Src	breast:	n/a	chr14:64763574-64763582 chr14:64763575-64763586 chr14:64763572-64763584 chr14:64763567-64763579 chr14:64763572-64763583
5	PBX3	chr14:64763502-64763671	GM12878	blood:	n/a	chr14:64763584-64763593
6	PBX3	chr14:64763308-64763696	SK-N-SH	brain:	n/a	chr14:64763318-64763329 chr14:64763584-64763593
7	FOS	chr14:64763393-64763738	MCF10A-Er-Src	breast:	n/a	chr14:64763574-64763582 chr14:64763575-64763586 chr14:64763572-64763584 chr14:64763567-64763579 chr14:64763572-64763583
8	NR3C1	chr14:64763243-64763658	A549	lung:	n/a	chr14:64763454-64763468 chr14:64763454-64763468 chr14:64763448-64763474 chr14:64763448-64763474 chr14:64763573-64763582 chr14:64763453-64763469 chr14:64763450-64763471 chr14:64763448-64763474 chr14:64763453-64763469 chr14:64763574-64763583 chr14:64763448-64763474 chr14:64763453-64763469 chr14:64763453-64763469 chr14:64763454-64763468
9	JUN	chr14:64763333-64763794	HUVEC	blood vessel:	n/a	chr14:64763574-64763582 chr14:64763575-64763586 chr14:64763572-64763584 chr14:64763567-64763579
10	BATF	chr14:64763398-64763710	GM12878	blood:	n/a	n/a
11	FOS	chr14:64763390-64763738	MCF10A-Er-Src	breast:	n/a	chr14:64763574-64763582 chr14:64763575-64763586 chr14:64763572-64763584 chr14:64763567-64763579 chr14:64763572-64763583
12	NR3C1	chr14:64763187-64763659	A549	lung:	n/a	chr14:64763454-64763468 chr14:64763454-64763468 chr14:64763448-64763474 chr14:64763448-64763474 chr14:64763573-64763582 chr14:64763453-64763469 chr14:64763450-64763471 chr14:64763448-64763474 chr14:64763453-64763469 chr14:64763574-64763583 chr14:64763448-64763474 chr14:64763453-64763469 chr14:64763453-64763469 chr14:64763454-64763468
13	PBX3	chr14:64763352-64763752	SK-N-SH	brain:	n/a	chr14:64763584-64763593
14	FOS	chr14:64763402-64763764	MCF10A-Er-Src	breast:	n/a	chr14:64763574-64763582 chr14:64763575-64763586 chr14:64763572-64763584 chr14:64763567-64763579 chr14:64763572-64763583
15	POLR2A	chr14:64763175-64763811	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:64762035..64765050-chr14:64765458..64769653,3	MCF-7	breast:
2	chr14:64611735..64614161-chr14:64762430..64763965,2	MCF-7	breast:

Variant related genes	Relation type
ESR2	TF binding region

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10143616	0.85[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs1152590	0.80[MEX][hapmap]
rs1152592	0.80[MEX][hapmap]
rs1152594	0.80[MEX][hapmap]
rs12323665	0.92[EUR][1000 genomes]
rs12435376	0.89[MEX][hapmap]
rs1262242	0.80[MEX][hapmap]
rs17101765	1.00[CEU][hapmap];0.95[GIH][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes]
rs17179740	0.89[GIH][hapmap]
rs2256191	0.89[MEX][hapmap]
rs2978381	0.91[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs3020444	1.00[CEU][hapmap];0.98[GIH][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes]
rs3020449	0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs3020450	1.00[CEU][hapmap];0.98[GIH][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes]
rs6573547	0.85[MEX][hapmap]
rs6573548	0.89[MEX][hapmap]
rs6573553	0.83[GIH][hapmap]
rs7148072	0.89[MEX][hapmap]
rs7154455	0.96[CEU][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs8011682	0.95[EUR][1000 genomes]
rs8020356	0.94[EUR][1000 genomes]
rs867443	0.83[CEU][hapmap]
rs872227	0.80[MEX][hapmap]

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	nsv902019	chr14:64395569-64882380	Enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv1307	chr14:64742037-64787315	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2987983	KCNH5	cis	parietal	SCAN
rs2987983	MTHFD1	cis	cerebellum	SCAN
rs2987983	MTHFD1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:64761800-64764400	Enhancers	HUVEC	blood vessel
2	chr14:64762000-64764000	Enhancers	Muscle Satellite Cultured Cells	--
3	chr14:64762000-64764000	Weak transcription	Brain Anterior Caudate	brain
4	chr14:64762000-64764400	Enhancers	NHEK	skin
5	chr14:64762600-64763800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr14:64762600-64764200	Enhancers	HMEC	breast
7	chr14:64762600-64764400	Enhancers	Thymus	Thymus
8	chr14:64762800-64763800	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr14:64763000-64763800	Enhancers	GM12878-XiMat	blood
10	chr14:64763000-64764200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr14:64763000-64764200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr14:64763000-64764200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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