Variant report

Variant	rs16963517
Chromosome Location	chr15:50548054-50548055
allele	A/G
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	GATA3	chr15:50548026-50549800	MCF-7	breast:	n/a	chr15:50549183-50549191 chr15:50549560-50549568
2	GATA3	chr15:50547943-50549854	MCF-7	breast:	n/a	chr15:50549183-50549191 chr15:50549560-50549568
3	NR2F2	chr15:50548009-50549566	MCF-7	breast:	n/a	n/a
4	GATA3	chr15:50547800-50549361	MCF-7	breast:	n/a	chr15:50549183-50549191
5	MAX	chr15:50547915-50549072	MCF-7	breast:	n/a	n/a
6	NR2F2	chr15:50548028-50549332	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:50533878..50537241-chr15:50547265..50550070,3	MCF-7	breast:
2	chr15:50547608..50550414-chr15:50649423..50651512,2	K562	blood:
3	chr15:50520136..50522623-chr15:50547396..50549245,2	MCF-7	breast:
4	chr15:50537515..50540113-chr15:50546589..50548323,2	MCF-7	breast:
5	chr15:50547893..50550558-chr15:50556837..50559575,2	MCF-7	breast:

Variant related genes	Relation type
HDC	TF binding region
ENSG00000241175	Chromatin interaction
ENSG00000140287	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1529341	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs1529342	0.86[EUR][1000 genomes]
rs1529343	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs1529344	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs1549521	1.00[CEU][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs16963474	0.86[EUR][1000 genomes]
rs16963477	0.86[EUR][1000 genomes]
rs16963514	1.00[ASW][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs2073440	1.00[CEU][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs2081629	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs28392818	1.00[EUR][1000 genomes]
rs28758988	0.86[EUR][1000 genomes]
rs34406040	1.00[EUR][1000 genomes]
rs56405312	0.86[EUR][1000 genomes]
rs57018658	1.00[EUR][1000 genomes]
rs57796210	0.86[EUR][1000 genomes]
rs58421641	0.86[EUR][1000 genomes]
rs6493418	1.00[CEU][hapmap];0.82[YRI][hapmap]
rs7166052	0.86[EUR][1000 genomes]
rs7166426	0.86[EUR][1000 genomes]
rs7166844	0.86[EUR][1000 genomes]
rs7166950	0.86[EUR][1000 genomes]
rs7167126	0.86[EUR][1000 genomes]
rs7167784	0.86[EUR][1000 genomes]
rs7168181	0.86[EUR][1000 genomes]
rs7183971	0.86[EUR][1000 genomes]
rs73397258	0.86[EUR][1000 genomes]
rs73397259	0.86[EUR][1000 genomes]
rs73397268	0.86[EUR][1000 genomes]
rs73397273	0.86[EUR][1000 genomes]
rs73397279	0.86[EUR][1000 genomes]
rs73397282	0.86[EUR][1000 genomes]
rs8024393	1.00[TSI][hapmap]
rs8028354	0.86[EUR][1000 genomes]
rs8040505	0.82[YRI][hapmap]
rs8042671	1.00[YRI][hapmap]

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	nsv1044277	chr15:49921547-50702386	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542380	chr15:49921547-50702386	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv1035983	chr15:50223334-50595170	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv542382	chr15:50223334-50595170	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:50532400-50549600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:50542200-50548200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr15:50542400-50548400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr15:50544600-50549200	Weak transcription	HSMMtube	muscle
5	chr15:50546400-50548600	Enhancers	Hela-S3	cervix
6	chr15:50548000-50548800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr15:50548000-50549000	Enhancers	A549	lung
8	chr15:50548000-50551800	Enhancers	K562	blood
9	chr15:50548000-50555600	Enhancers	Primary neutrophils fromperipheralblood	blood

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