Variant report

Variant	rs2582531
Chromosome Location	chr14:105392533-105392534
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	STAT5A	chr14:105392481-105393382	GM12878	blood:	n/a	n/a
2	POLR2A	chr14:105392089-105393339	GM19193	blood:	n/a	n/a
3	MTA3	chr14:105390644-105393638	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:105387983..105391489-chr14:105392006..105395629,4	MCF-7	breast:
2	chr14:105391507..105394096-chr14:105419228..105421927,2	MCF-7	breast:
3	chr14:105391640..105393998-chr14:105436679..105438519,2	MCF-7	breast:
4	chr14:105387917..105389579-chr14:105391282..105393689,2	K562	blood:

Variant related genes	Relation type
PLD4	TF binding region
ENSG00000166428	Chromatin interaction
ENSG00000185567	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10083374	0.81[EUR][1000 genomes]
rs10083490	0.89[CHB][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs10083496	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10141053	0.89[EUR][1000 genomes]
rs10149193	0.82[EUR][1000 genomes]
rs10152073	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1036713	0.89[CHB][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10438246	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10438247	0.81[EUR][1000 genomes]
rs1048257	0.89[CHB][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs11160825	0.82[EUR][1000 genomes]
rs11623422	0.89[CHB][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs11848564	0.83[EUR][1000 genomes]
rs11851053	0.89[CHB][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs12885004	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2582529	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2582533	0.89[CHB][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2819419	0.89[CHB][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2819422	0.82[EUR][1000 genomes]
rs2819424	0.82[EUR][1000 genomes]
rs2819439	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2819468	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2819469	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28380382	0.82[EUR][1000 genomes]
rs2841268	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2841269	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2841276	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2841277	0.95[CHB][hapmap];0.85[JPT][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2841278	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2841280	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2841281	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28454709	0.82[EUR][1000 genomes]
rs28600075	0.82[EUR][1000 genomes]
rs2919624	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3001424	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34499888	0.80[EUR][1000 genomes]
rs3742935	0.89[CHB][hapmap];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4264326	0.81[EUR][1000 genomes]
rs4465542	0.82[EUR][1000 genomes]
rs61421370	0.90[EUR][1000 genomes]
rs8004038	0.80[EUR][1000 genomes]
rs874753	0.96[EUR][1000 genomes]
rs879448	0.92[CEU][hapmap];0.97[EUR][1000 genomes]
rs9671643	0.81[EUR][1000 genomes]
rs9672139	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053591	chr14:105024558-105475931	Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
2	nsv542224	chr14:105024558-105475931	Bivalent Enhancer Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
3	esv1828345	chr14:105100787-105803170	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
4	nsv542225	chr14:105133688-105803170	Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
5	nsv542227	chr14:105157572-105803170	Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	147 gene(s)	inside rSNPs	diseases
6	nsv456456	chr14:105285159-105412541	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	nsv566099	chr14:105285159-105412541	Bivalent Enhancer Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
8	nsv917106	chr14:105339195-105803170	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
9	nsv566139	chr14:105347296-105417147	Weak transcription Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
10	nsv902419	chr14:105381763-105494262	Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
11	nsv1049253	chr14:105384959-105471855	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
12	nsv542228	chr14:105390569-105459912	Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2582531	TDRD9	cis	Thyroid	GTEx

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:105390800-105392600	Enhancers	Placenta	Placenta
2	chr14:105390800-105393600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
3	chr14:105390800-105393600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr14:105390800-105393600	Flanking Active TSS	GM12878-XiMat	blood
5	chr14:105390800-105393600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
6	chr14:105390800-105394000	Flanking Active TSS	Primary B cells from cord blood	blood
7	chr14:105391000-105393200	Flanking Active TSS	Primary hematopoietic stem cells	blood
8	chr14:105391000-105394000	Weak transcription	Stomach Smooth Muscle	stomach
9	chr14:105391000-105395400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr14:105391200-105392600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
11	chr14:105391200-105393000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
12	chr14:105391200-105393600	Flanking Active TSS	Primary B cells from peripheral blood	blood
13	chr14:105391200-105393600	Enhancers	Adipose Nuclei	Adipose
14	chr14:105391200-105393600	Active TSS	Brain Hippocampus Middle	brain
15	chr14:105391200-105394200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
16	chr14:105391400-105392600	Enhancers	Fetal Intestine Large	intestine
17	chr14:105391600-105392600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr14:105391600-105393000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr14:105391600-105394200	Enhancers	Fetal Thymus	thymus
20	chr14:105391600-105395000	Enhancers	Fetal Intestine Small	intestine
21	chr14:105391600-105398600	Weak transcription	Gastric	stomach
22	chr14:105391800-105392600	Enhancers	Colonic Mucosa	Colon
23	chr14:105391800-105394200	Enhancers	Spleen	Spleen
24	chr14:105392000-105392800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr14:105392000-105392800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr14:105392200-105393000	Enhancers	H1 Cell Line	embryonic stem cell
27	chr14:105392200-105393000	Enhancers	NH-A	brain
28	chr14:105392200-105394200	Enhancers	Fetal Muscle Leg	muscle
29	chr14:105392200-105395800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr14:105392400-105392600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr14:105392400-105392600	Active TSS	Rectal Mucosa Donor 29	rectum
32	chr14:105392400-105392800	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
33	chr14:105392400-105392800	Flanking Active TSS	Duodenum Mucosa	Duodenum

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