Variant report

Variant	rs12453343
Chromosome Location	chr17:38181176-38181177
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr17:38181167-38181568	MCF10A-Er-Src	breast:	n/a	n/a
2	STAT3	chr17:38181172-38181531	MCF10A-Er-Src	breast:	n/a	n/a
3	STAT3	chr17:38181163-38181546	MCF10A-Er-Src	breast:	n/a	n/a
4	USF1	chr17:38181118-38181465	ECC-1	luminal epithelium:	n/a	n/a
5	POLR2A	chr17:38181160-38181608	U87	brain:	n/a	n/a
6	STAT3	chr17:38181166-38181545	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:38178740..38181888-chr17:38181920..38184770,3	K562	blood:
2	chr17:38180102..38182541-chr17:38472880..38475215,2	MCF-7	breast:
3	chr17:38178218..38182497-chr17:38276428..38279757,5	MCF-7	breast:
4	chr17:38176819..38178411-chr17:38180264..38182025,2	K562	blood:
5	chr17:38178625..38181576-chr17:38444051..38445917,2	K562	blood:
6	chr17:38175295..38180645-chr17:38181007..38185256,8	MCF-7	breast:

No data

Variant related genes	Relation type
MED24	TF binding region
ENSG00000008838	Chromatin interaction
ENSG00000238793	Chromatin interaction
ENSG00000188895	Chromatin interaction
ENSG00000131759	Chromatin interaction
ENSG00000094804	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10445310	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11078930	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11078931	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11078935	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11078936	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11654208	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11655264	0.89[ASN][1000 genomes]
rs11655655	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11658328	0.91[ASN][1000 genomes]
rs11867302	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12309	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12450800	0.87[ASN][1000 genomes]
rs12451547	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12451897	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12453334	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12453341	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12453764	0.89[ASN][1000 genomes]
rs12601929	0.87[ASN][1000 genomes]
rs12602514	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12602854	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12939682	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12940405	0.89[ASN][1000 genomes]
rs2227319	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2227321	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2227333	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2241244	0.91[ASN][1000 genomes]
rs2241245	0.91[ASN][1000 genomes]
rs2270401	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2302774	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2302776	0.81[ASN][1000 genomes]
rs2302777	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2305481	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2305482	0.87[ASN][1000 genomes]
rs25645	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3087852	0.89[ASN][1000 genomes]
rs34003767	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34342173	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34453912	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34540281	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34648856	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34933056	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35272691	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35982947	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs36071767	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3744245	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3785550	0.87[ASN][1000 genomes]
rs3816472	0.90[ASN][1000 genomes]
rs3859187	0.91[ASN][1000 genomes]
rs3859189	0.89[ASN][1000 genomes]
rs3935281	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4065321	0.90[ASN][1000 genomes]
rs4072639	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4433838	0.90[ASN][1000 genomes]
rs66826786	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7502971	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8066582	0.91[ASN][1000 genomes]
rs8070444	0.91[ASN][1000 genomes]
rs8071037	0.91[ASN][1000 genomes]
rs8073254	0.91[ASN][1000 genomes]
rs8075668	0.89[ASN][1000 genomes]
rs9898547	0.87[ASN][1000 genomes]
rs9915252	0.90[ASN][1000 genomes]
rs9916158	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492308	chr17:38033039-38204458	Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12453343	MED24	cis	Muscle Skeletal	GTEx
rs12453343	GSDMA	cis	Nerve Tibial	GTEx
rs12453343	GSDMA	cis	Thyroid	GTEx
rs12453343	GSDMA	cis	Esophagus Muscularis	GTEx
rs12453343	GSDMA	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38166800-38181600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr17:38170400-38181600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr17:38171400-38186000	Weak transcription	Small Intestine	intestine
4	chr17:38173000-38181400	Weak transcription	Fetal Kidney	kidney
5	chr17:38173400-38183800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr17:38173400-38192800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr17:38173600-38182000	Strong transcription	Thymus	Thymus
8	chr17:38173800-38181400	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr17:38173800-38181800	Strong transcription	Primary T cells from cord blood	blood
10	chr17:38173800-38182400	Strong transcription	Duodenum Mucosa	Duodenum
11	chr17:38174000-38192600	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr17:38174000-38193800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr17:38174200-38183200	Strong transcription	Placenta	Placenta
14	chr17:38174200-38183400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr17:38174200-38183400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr17:38174200-38187400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr17:38174400-38183200	Strong transcription	Primary B cells from peripheral blood	blood
18	chr17:38174400-38193200	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr17:38174600-38181400	Strong transcription	Primary T helper cells PMA-I stimulated	--
20	chr17:38174600-38181800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr17:38174600-38182000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr17:38174800-38181400	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr17:38174800-38192600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr17:38175000-38193800	Strong transcription	HepG2	liver
25	chr17:38175200-38181600	Strong transcription	Fetal Thymus	thymus
26	chr17:38175200-38182800	Strong transcription	Brain Angular Gyrus	brain
27	chr17:38175200-38192600	Strong transcription	Fetal Brain Female	brain
28	chr17:38175200-38193200	Strong transcription	Dnd41	blood
29	chr17:38175400-38182200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr17:38175400-38188200	Weak transcription	Fetal Heart	heart
31	chr17:38175600-38181800	Weak transcription	Fetal Brain Male	brain
32	chr17:38175600-38191400	Strong transcription	Brain Hippocampus Middle	brain
33	chr17:38175600-38193200	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr17:38175600-38193200	Strong transcription	Brain Cingulate Gyrus	brain
35	chr17:38175600-38193800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr17:38175800-38182400	Strong transcription	Liver	Liver
37	chr17:38175800-38183400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
38	chr17:38175800-38192600	Strong transcription	Brain Germinal Matrix	brain
39	chr17:38176000-38189800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr17:38176000-38192600	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr17:38176000-38195400	Weak transcription	Right Atrium	heart
42	chr17:38176200-38183400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr17:38176200-38183400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr17:38176200-38193800	Strong transcription	Cortex derived primary cultured neurospheres	brain
45	chr17:38176400-38192400	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr17:38176600-38183000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr17:38177400-38184000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr17:38177600-38183200	Strong transcription	H9 Cell Line	embryonic stem cell
49	chr17:38177800-38183000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr17:38177800-38185400	Strong transcription	GM12878-XiMat	blood

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