Variant report

Variant	rs2929710
Chromosome Location	chr5:17213365-17213366
allele	A/C
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	NR3C1	chr5:17213124-17213507	A549	lung:	n/a	chr5:17213297-17213310
2	FOXA1	chr5:17213118-17213402	T-47D	breast:	n/a	n/a
3	NR3C1	chr5:17213103-17213470	A549	lung:	n/a	chr5:17213297-17213310
4	GATA3	chr5:17213100-17213640	MCF-7	breast:	n/a	chr5:17213247-17213256 chr5:17213246-17213256
5	GATA3	chr5:17213138-17213428	MCF-7	breast:	n/a	chr5:17213247-17213256 chr5:17213246-17213256
6	GATA3	chr5:17213009-17213453	MCF-7	breast:	n/a	chr5:17213247-17213256 chr5:17213246-17213256
7	GATA3	chr5:17213177-17213435	MCF-7	breast:	n/a	chr5:17213247-17213256 chr5:17213246-17213256
8	FOXA1	chr5:17213121-17213391	T-47D	breast:	n/a	n/a
9	GATA3	chr5:17213124-17213422	T-47D	breast:	n/a	chr5:17213247-17213256 chr5:17213246-17213256
10	MAX	chr5:17213084-17213517	MCF-7	breast:	n/a	n/a
11	ESR1	chr5:17213084-17213483	T-47D	breast:	n/a	chr5:17213291-17213308
12	ESR1	chr5:17213106-17213421	T-47D	breast:	n/a	chr5:17213291-17213308
13	NR2F2	chr5:17213115-17213579	MCF-7	breast:	n/a	n/a
14	GATA3	chr5:17213130-17213446	T-47D	breast:	n/a	chr5:17213247-17213256 chr5:17213246-17213256
15	SIN3AK20	chr5:17213042-17213678	MCF-7	breast:	n/a	n/a

Variant related genes	Relation type
BASP1	TF binding region

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs2929709	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2929726	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2956564	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2962370	0.80[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025225	chr5:16714512-17234866	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv880277	chr5:16829442-17316288	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv830218	chr5:17093162-17290045	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv1029959	chr5:17133214-17455995	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
5	nsv4738	chr5:17178267-17223677	Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv521697	chr5:17211649-17225333	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2929710	MARCH11	cis	cerebellum	SCAN
rs2929710	LOC285696	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:17200000-17216200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr5:17209600-17213600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:17211000-17213400	Enhancers	Fetal Brain Male	brain
4	chr5:17212000-17215800	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr5:17212400-17214400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
6	chr5:17212400-17215600	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr5:17212400-17216600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr5:17212600-17213400	Enhancers	Stomach Mucosa	stomach
9	chr5:17213000-17214000	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr5:17213000-17214000	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr5:17213000-17214400	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr5:17213000-17214600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr5:17213000-17215000	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr5:17213000-17215000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr5:17213000-17215400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr5:17213200-17213400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr5:17213200-17213400	Flanking Active TSS	Brain Germinal Matrix	brain
18	chr5:17213200-17213400	Transcr. at gene 5' and 3'	A549	lung
19	chr5:17213200-17213400	Genic enhancers	Hela-S3	cervix
20	chr5:17213200-17213600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr5:17213200-17213600	Flanking Active TSS	Fetal Brain Female	brain
22	chr5:17213200-17213800	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr5:17213200-17214000	Enhancers	HUES48 Cell Line	embryonic stem cell
24	chr5:17213200-17214200	Enhancers	ES-I3 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links