Variant report

Variant	rs1326426
Chromosome Location	chr13:89275195-89275196
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	FOS	chr13:89275078-89275260	MCF10A-Er-Src	breast:	n/a	n/a
2	SETDB1	chr13:89274870-89275301	U2OS	brain:	n/a	n/a
3	FOS	chr13:89275026-89275279	MCF10A-Er-Src	breast:	n/a	n/a
4	KAP1	chr13:89274881-89275241	HEK293	kidney:	n/a	n/a
5	FOS	chr13:89275016-89275333	MCF10A-Er-Src	breast:	n/a	n/a
6	FOS	chr13:89275036-89275333	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:89273831..89276576-chr13:89278587..89280292,2	MCF-7	breast:

Variant related genes	Relation type
LINC00560	TF binding region
ENSG00000261666	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs12427865	0.81[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12853631	0.83[ASN][1000 genomes]
rs1326421	0.87[ASN][1000 genomes]
rs1326422	0.88[ASN][1000 genomes]
rs1326423	0.96[ASN][1000 genomes]
rs1326424	0.93[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1326427	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1326428	0.91[ASN][1000 genomes]
rs1326444	0.93[ASN][1000 genomes]
rs1409452	0.88[ASN][1000 genomes]
rs1409453	0.89[ASN][1000 genomes]
rs1409454	0.88[ASN][1000 genomes]
rs1536355	0.91[ASN][1000 genomes]
rs1536356	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1536357	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1536358	0.91[ASN][1000 genomes]
rs1853978	0.84[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs1952189	0.88[ASN][1000 genomes]
rs2038934	0.95[ASN][1000 genomes]
rs2038935	0.96[ASN][1000 genomes]
rs2225048	0.88[ASN][1000 genomes]
rs4293239	0.84[AFR][1000 genomes]
rs4310727	0.84[AFR][1000 genomes]
rs4447288	0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4519197	0.83[ASN][1000 genomes]
rs4547212	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6492230	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7326991	0.83[ASN][1000 genomes]
rs7330466	0.89[ASN][1000 genomes]
rs7335014	0.87[ASN][1000 genomes]
rs7335817	0.89[ASN][1000 genomes]
rs7983711	0.85[ASN][1000 genomes]
rs7983924	0.88[ASN][1000 genomes]
rs7987127	0.89[ASN][1000 genomes]
rs7987540	0.88[ASN][1000 genomes]
rs7993257	0.86[ASN][1000 genomes]
rs8000708	0.96[ASN][1000 genomes]
rs8000777	0.88[ASN][1000 genomes]
rs8002705	0.89[ASN][1000 genomes]
rs9301420	0.80[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9301421	0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9515129	0.88[ASN][1000 genomes]
rs9521545	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9521558	0.88[ASN][1000 genomes]
rs9521561	0.88[ASN][1000 genomes]
rs9588008	0.83[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	nsv870345	chr13:89164439-89295782	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1051177	chr13:89219432-89359036	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv900816	chr13:89224649-89392881	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1051359	chr13:89258679-89311805	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1326426	ECHDC1	trans	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:89273800-89276000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr13:89274000-89276400	Enhancers	Primary T cells from cord blood	blood
3	chr13:89274400-89275600	Enhancers	NHEK	skin
4	chr13:89274400-89275800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr13:89274600-89275200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
6	chr13:89274800-89275200	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr13:89274800-89275200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
8	chr13:89274800-89276000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr13:89275000-89276600	Enhancers	Primary T helper naive cells from peripheral blood	blood

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