Variant report

Variant	rs9916158
Chromosome Location	chr17:38182229-38182230
allele	G/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	POLR2A	chr17:38182211-38182374	K562	blood:	n/a	n/a
2	GATA3	chr17:38182229-38182916	MCF-7	breast:	n/a	n/a
3	FOS	chr17:38182139-38182428	MCF10A-Er-Src	breast:	n/a	n/a
4	STAT3	chr17:38182220-38182911	MCF10A-Er-Src	breast:	n/a	chr17:38182767-38182775
5	STAT3	chr17:38182220-38182908	MCF10A-Er-Src	breast:	n/a	chr17:38182767-38182775
6	MAFK	chr17:38182134-38182263	Hela-S3	cervix:	n/a	chr17:38182252-38182262 chr17:38182252-38182261
7	POLR2A	chr17:38181978-38182724	HUVEC	blood vessel:	n/a	n/a
8	MAFK	chr17:38182141-38182402	HepG2	liver:	n/a	chr17:38182348-38182364 chr17:38182252-38182262 chr17:38182349-38182360 chr17:38182252-38182261 chr17:38182347-38182361
9	FOS	chr17:38182080-38182982	MCF10A-Er-Src	breast:	n/a	n/a
10	MAFK	chr17:38182166-38182371	IMR90	lung:	n/a	chr17:38182348-38182364 chr17:38182252-38182262 chr17:38182349-38182360 chr17:38182252-38182261 chr17:38182347-38182361
11	STAT3	chr17:38182070-38182278	MCF10A-Er-Src	breast:	n/a	n/a
12	MAFF	chr17:38182210-38182401	HepG2	liver:	n/a	chr17:38182245-38182263
13	MYC	chr17:38182218-38182970	MCF10A-Er-Src	breast:	n/a	n/a
14	FOS	chr17:38182218-38183006	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:38170232..38173097-chr17:38181812..38184113,4	MCF-7	breast:
2	chr17:38170609..38173071-chr17:38181273..38184131,2	MCF-7	breast:
3	chr17:38180102..38182541-chr17:38472880..38475215,2	MCF-7	breast:
4	chr17:38181477..38183501-chr17:38217583..38219827,2	MCF-7	breast:
5	chr17:38178218..38182497-chr17:38276428..38279757,5	MCF-7	breast:
6	chr17:38178740..38181888-chr17:38181920..38184770,3	K562	blood:
7	chr17:38177803..38180808-chr17:38181920..38184987,3	K562	blood:
8	chr17:38181641..38185122-chr17:38333882..38336606,4	MCF-7	breast:
9	chr17:38175295..38180645-chr17:38181007..38185256,8	MCF-7	breast:

Variant related genes	Relation type
MED24	TF binding region
ENSG00000265799	Chromatin interaction
ENSG00000188895	Chromatin interaction
ENSG00000131759	Chromatin interaction
ENSG00000008838	Chromatin interaction
ENSG00000108352	Chromatin interaction
ENSG00000126351	Chromatin interaction
ENSG00000108342	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10445310	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11078930	0.87[JPT][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11078931	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11078935	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11078936	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11654208	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11655264	1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs11655655	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11658328	0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11867302	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12309	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12450800	0.86[ASN][1000 genomes]
rs12451547	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12451897	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12453334	0.83[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12453341	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12453343	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12453764	0.88[ASN][1000 genomes]
rs12601929	0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12602514	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12602854	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12939682	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12940405	0.88[ASN][1000 genomes]
rs2227319	0.87[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2227321	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2227333	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2241244	0.90[ASN][1000 genomes]
rs2241245	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2270401	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2302774	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2302776	1.00[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs2302777	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2305481	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2305482	0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs25645	0.92[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3087852	0.88[ASN][1000 genomes]
rs34003767	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34342173	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34453912	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34540281	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34648856	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34933056	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35272691	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35982947	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs36071767	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3744245	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3785550	0.87[ASN][1000 genomes]
rs3816472	0.89[ASN][1000 genomes]
rs3859187	0.90[ASN][1000 genomes]
rs3859189	0.88[ASN][1000 genomes]
rs3935281	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4065321	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4072639	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4433838	0.89[ASN][1000 genomes]
rs66826786	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7502971	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8066582	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs8070444	0.90[ASN][1000 genomes]
rs8071037	0.90[ASN][1000 genomes]
rs8073254	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs8075668	1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs8077456	0.84[JPT][hapmap]
rs9898547	0.87[ASN][1000 genomes]
rs9915252	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs9916158	CCL2	cis	cerebellum	SCAN
rs9916158	GSDMA	cis	Adipose Subcutaneous	GTEx
rs9916158	MED24	cis	cerebellum	SCAN
rs9916158	MED24	cis	Muscle Skeletal	GTEx
rs9916158	GSDMA	cis	Esophagus Muscularis	GTEx
rs9916158	PSMD3	cis	parietal	SCAN
rs9916158	MED24	cis	parietal	SCAN
rs9916158	PCGF2	cis	cerebellum	SCAN
rs9916158	KRT222	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38171400-38186000	Weak transcription	Small Intestine	intestine
2	chr17:38173400-38183800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr17:38173400-38192800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr17:38173800-38182400	Strong transcription	Duodenum Mucosa	Duodenum
5	chr17:38174000-38192600	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr17:38174000-38193800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr17:38174200-38183200	Strong transcription	Placenta	Placenta
8	chr17:38174200-38183400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr17:38174200-38183400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr17:38174200-38187400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr17:38174400-38183200	Strong transcription	Primary B cells from peripheral blood	blood
12	chr17:38174400-38193200	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr17:38174800-38192600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr17:38175000-38193800	Strong transcription	HepG2	liver
15	chr17:38175200-38182800	Strong transcription	Brain Angular Gyrus	brain
16	chr17:38175200-38192600	Strong transcription	Fetal Brain Female	brain
17	chr17:38175200-38193200	Strong transcription	Dnd41	blood
18	chr17:38175400-38188200	Weak transcription	Fetal Heart	heart
19	chr17:38175600-38191400	Strong transcription	Brain Hippocampus Middle	brain
20	chr17:38175600-38193200	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr17:38175600-38193200	Strong transcription	Brain Cingulate Gyrus	brain
22	chr17:38175600-38193800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr17:38175800-38182400	Strong transcription	Liver	Liver
24	chr17:38175800-38183400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
25	chr17:38175800-38192600	Strong transcription	Brain Germinal Matrix	brain
26	chr17:38176000-38189800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr17:38176000-38192600	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr17:38176000-38195400	Weak transcription	Right Atrium	heart
29	chr17:38176200-38183400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr17:38176200-38183400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr17:38176200-38193800	Strong transcription	Cortex derived primary cultured neurospheres	brain
32	chr17:38176400-38192400	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr17:38176600-38183000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr17:38177400-38184000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr17:38177600-38183200	Strong transcription	H9 Cell Line	embryonic stem cell
36	chr17:38177800-38183000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr17:38177800-38185400	Strong transcription	GM12878-XiMat	blood
38	chr17:38177800-38191000	Strong transcription	H1 Cell Line	embryonic stem cell
39	chr17:38178000-38187800	Strong transcription	Right Ventricle	heart
40	chr17:38178200-38183200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr17:38178200-38192600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr17:38178400-38182800	Strong transcription	Placenta Amnion	Placenta Amnion
43	chr17:38178400-38183200	Strong transcription	Brain Inferior Temporal Lobe	brain
44	chr17:38178600-38183000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr17:38178600-38191200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr17:38178800-38184600	Weak transcription	HSMMtube	muscle
47	chr17:38179000-38184000	Genic enhancers	Muscle Satellite Cultured Cells	--
48	chr17:38179000-38192600	Strong transcription	Primary neutrophils fromperipheralblood	blood
49	chr17:38179200-38183200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr17:38179800-38182400	Strong transcription	Spleen	Spleen

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