Variant report

Variant	rs12309
Chromosome Location	chr17:38175462-38175463
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:24)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr17:38175457-38176032	MCF10A-Er-Src	breast:	n/a	n/a
2	MYC	chr17:38174868-38175869	MCF10A-Er-Src	breast:	n/a	chr17:38174944-38174954
3	MXI1	chr17:38175320-38176027	IMR90	lung:	n/a	n/a
4	CTCF	chr17:38175380-38175530	HPF	lung:	n/a	n/a
5	STAT3	chr17:38175456-38176048	MCF10A-Er-Src	breast:	n/a	n/a
6	FOS	chr17:38175406-38176036	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr17:38175260-38175923	HUVEC	blood vessel:	n/a	n/a
8	POLR2A	chr17:38170916-38176213	MCF10A-Er-Src	breast:	n/a	n/a
9	FOS	chr17:38173937-38175874	MCF10A-Er-Src	breast:	n/a	chr17:38174947-38174956
10	POLR2A	chr17:38170766-38176716	U87	brain:	n/a	n/a
11	POLR2A	chr17:38170628-38176722	U87	brain:	n/a	n/a
12	POLR2A	chr17:38171303-38175657	MCF10A-Er-Src	breast:	n/a	n/a
13	STAT3	chr17:38175233-38175847	MCF10A-Er-Src	breast:	n/a	n/a
14	POLR2A	chr17:38175414-38176036	HUVEC	blood vessel:	n/a	n/a
15	POLR2A	chr17:38173854-38176132	HUVEC	blood vessel:	n/a	n/a
16	POLR2A	chr17:38174089-38176121	HUVEC	blood vessel:	n/a	n/a
17	MYC	chr17:38175207-38175870	MCF10A-Er-Src	breast:	n/a	n/a
18	POLR2A	chr17:38175272-38175563	HepG2	liver:	n/a	n/a
19	POLR2A	chr17:38171205-38176070	U87	brain:	n/a	n/a
20	POLR2A	chr17:38173976-38176162	HUVEC	blood vessel:	n/a	n/a
21	NR3C1	chr17:38174958-38175533	A549	lung:	n/a	chr17:38175300-38175314
22	MYC	chr17:38175440-38175905	HUVEC	blood vessel:	n/a	n/a
23	E2F4	chr17:38175446-38175794	MCF10A-Er-Src	breast:	n/a	n/a
24	CTCF	chr17:38175420-38175570	BJ	skin:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:38174242..38176838-chr17:38278779..38280861,2	MCF-7	breast:
2	chr17:38172520..38175725-chr17:38187607..38191443,4	MCF-7	breast:
3	chr17:38175295..38180645-chr17:38181007..38185256,8	MCF-7	breast:
4	chr17:38174715..38177590-chr17:38209751..38212777,3	K562	blood:
5	chr17:38175071..38177613-chr17:38178105..38180812,3	MCF-7	breast:
6	chr17:38169328..38171805-chr17:38172299..38175519,5	K562	blood:
7	chr17:38174842..38178903-chr17:38208625..38211251,3	K562	blood:
8	chr17:38172859..38176802-chr17:38178682..38181500,4	K562	blood:
9	chr17:38141745..38144493-chr17:38173834..38176591,2	MCF-7	breast:
10	chr17:38173047..38175621-chr17:38177692..38179979,3	MCF-7	breast:
11	chr17:38171100..38173173-chr17:38173231..38176436,3	K562	blood:
12	chr17:38169328..38171032-chr17:38172943..38175519,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000265799	TF binding region
ENSG00000188895	Chromatin interaction
ENSG00000238793	Chromatin interaction
ENSG00000108344	Chromatin interaction
ENSG00000008838	Chromatin interaction
ENSG00000108342	Chromatin interaction
ENSG00000265799	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 10 )

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

rs_ID	r²[population]
rs10445310	0.86[ASN][1000 genomes]
rs11078930	0.80[CEU][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11078931	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11078935	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11078936	0.91[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.87[TSI][hapmap];0.87[ASN][1000 genomes]
rs11654208	0.87[ASN][1000 genomes]
rs11655264	0.95[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs11655655	0.87[ASN][1000 genomes]
rs11658328	0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11867302	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12450800	0.85[ASN][1000 genomes]
rs12451547	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12451897	1.00[CEU][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12453334	0.89[ASW][hapmap];0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.81[LWK][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12453341	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12453343	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12453764	0.87[ASN][1000 genomes]
rs12601929	0.91[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.81[LWK][hapmap];0.85[TSI][hapmap];0.85[ASN][1000 genomes]
rs12602514	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12602854	0.85[ASN][1000 genomes]
rs12939682	0.87[ASN][1000 genomes]
rs12940405	0.87[ASN][1000 genomes]
rs2227319	0.82[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2227321	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2227333	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2241244	0.89[ASN][1000 genomes]
rs2241245	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2270401	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2302774	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2302776	0.95[CHB][hapmap];0.90[JPT][hapmap];0.81[TSI][hapmap]
rs2302777	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2305481	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2305482	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs25645	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[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];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3087852	0.87[ASN][1000 genomes]
rs34003767	0.87[ASN][1000 genomes]
rs34342173	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34453912	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34540281	0.85[ASN][1000 genomes]
rs34648856	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34933056	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35272691	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35982947	0.85[ASN][1000 genomes]
rs36071767	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3744245	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3785550	0.87[ASN][1000 genomes]
rs3816472	0.89[ASN][1000 genomes]
rs3859187	0.89[ASN][1000 genomes]
rs3859189	0.87[ASN][1000 genomes]
rs3935281	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4065321	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4072639	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4433838	0.89[ASN][1000 genomes]
rs66826786	0.86[ASN][1000 genomes]
rs7502971	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8066582	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs8070444	0.89[ASN][1000 genomes]
rs8071037	0.89[ASN][1000 genomes]
rs8073254	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs8075668	0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs8077456	0.84[JPT][hapmap]
rs9898547	0.86[ASN][1000 genomes]
rs9915252	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9916158	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]

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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs12309	MED24	cis	Muscle Skeletal	GTEx
rs12309	PCGF2	cis	cerebellum	SCAN
rs12309	MED24	cis	parietal	SCAN
rs12309	GSDMA	cis	Adipose Subcutaneous	GTEx
rs12309	PSMD3	cis	parietal	SCAN
rs12309	GSDMA	cis	Esophagus Muscularis	GTEx
rs12309	KRT222	cis	cerebellum	SCAN
rs12309	CCL2	cis	cerebellum	SCAN
rs12309	GSDMA	cis	Nerve Tibial	GTEx
rs12309	MED24	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38166800-38177400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr17:38166800-38178200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr17:38166800-38181600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr17:38169800-38175600	Enhancers	Fetal Lung	lung
5	chr17:38169800-38176000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr17:38170000-38175600	Weak transcription	Brain Cingulate Gyrus	brain
7	chr17:38170000-38176000	Enhancers	Ovary	ovary
8	chr17:38170000-38178800	Enhancers	Primary neutrophils fromperipheralblood	blood
9	chr17:38170200-38175600	Weak transcription	Brain Substantia Nigra	brain
10	chr17:38170200-38175800	Weak transcription	Primary B cells from cord blood	blood
11	chr17:38170400-38177600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr17:38170400-38181600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr17:38171200-38175600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr17:38171400-38186000	Weak transcription	Small Intestine	intestine
15	chr17:38171600-38176800	Weak transcription	Hela-S3	cervix
16	chr17:38172000-38175600	Weak transcription	GM12878-XiMat	blood
17	chr17:38172200-38176000	Enhancers	HUVEC	blood vessel
18	chr17:38172400-38175600	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr17:38172400-38175800	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr17:38172400-38178400	Weak transcription	Primary hematopoietic stem cells	blood
21	chr17:38172800-38176800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr17:38173000-38176600	Genic enhancers	Fetal Stomach	stomach
23	chr17:38173000-38179600	Strong transcription	Fetal Intestine Small	intestine
24	chr17:38173000-38181400	Weak transcription	Fetal Kidney	kidney
25	chr17:38173200-38176800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr17:38173400-38183800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr17:38173400-38192800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr17:38173600-38176600	Enhancers	Psoas Muscle	Psoas
29	chr17:38173600-38180200	Genic enhancers	Fetal Muscle Trunk	muscle
30	chr17:38173600-38180400	Genic enhancers	NHLF	lung
31	chr17:38173600-38182000	Strong transcription	Thymus	Thymus
32	chr17:38173800-38175800	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr17:38173800-38176000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr17:38173800-38176000	Enhancers	Right Atrium	heart
35	chr17:38173800-38176800	Enhancers	Stomach Mucosa	stomach
36	chr17:38173800-38179400	Strong transcription	Fetal Intestine Large	intestine
37	chr17:38173800-38179800	Genic enhancers	Spleen	Spleen
38	chr17:38173800-38180600	Strong transcription	Brain Anterior Caudate	brain
39	chr17:38173800-38181400	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr17:38173800-38181800	Strong transcription	Primary T cells from cord blood	blood
41	chr17:38173800-38182400	Strong transcription	Duodenum Mucosa	Duodenum
42	chr17:38174000-38175800	Enhancers	H1 Cell Line	embryonic stem cell
43	chr17:38174000-38175800	Enhancers	Colon Smooth Muscle	Colon
44	chr17:38174000-38176000	Genic enhancers	HUES6 Cell Line	embryonic stem cell
45	chr17:38174000-38176000	Weak transcription	Aorta	Aorta
46	chr17:38174000-38176600	Strong transcription	Rectal Mucosa Donor 31	rectum
47	chr17:38174000-38178200	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr17:38174000-38192600	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr17:38174000-38193800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr17:38174200-38175600	Enhancers	ES-I3 Cell Line	embryonic stem cell

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