Variant report

Variant	rs1049553
Chromosome Location	chr18:9475146-9475147
allele	C/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	NRF1	chr18:9474843-9475788	GM12878	blood:	n/a	chr18:9475490-9475504 chr18:9475295-9475304 chr18:9475212-9475223 chr18:9475213-9475224 chr18:9475213-9475222 chr18:9475492-9475501 chr18:9475490-9475501 chr18:9475210-9475224 chr18:9475487-9475501
2	PAX5	chr18:9474940-9476037	GM12892	blood:	n/a	chr18:9475491-9475500
3	POLR2A	chr18:9474863-9476076	HepG2	liver:	n/a	n/a
4	TEAD4	chr18:9474446-9475881	K562	blood:	n/a	n/a
5	YY1	chr18:9474934-9475984	GM12892	blood:	n/a	n/a
6	SP1	chr18:9475138-9476082	GM12878	blood:	n/a	chr18:9475551-9475560 chr18:9475829-9475843 chr18:9475475-9475489 chr18:9475839-9475851 chr18:9475840-9475850 chr18:9475550-9475562 chr18:9475550-9475562 chr18:9475839-9475851 chr18:9475833-9475842 chr18:9475552-9475561 chr18:9475840-9475850 chr18:9475552-9475561 chr18:9475833-9475843
7	USF1	chr18:9475094-9475702	K562	blood:	n/a	n/a
8	POLR2A	chr18:9474722-9476003	H1-neurons	neurons:	n/a	n/a
9	TEAD4	chr18:9474476-9475882	ECC-1	luminal epithelium:	n/a	n/a
10	RELA	chr18:9474789-9475903	GM18951	blood:	n/a	n/a
11	USF1	chr18:9474979-9475573	ECC-1	luminal epithelium:	n/a	n/a
12	WRNIP1	chr18:9474956-9475898	GM12878	blood:	n/a	n/a
13	ELK1	chr18:9474802-9475891	Hela-S3	cervix:	n/a	n/a
14	HEY1	chr18:9474879-9476043	HepG2	liver:	n/a	chr18:9475763-9475778 chr18:9474965-9474980
15	YY1	chr18:9474916-9476074	HepG2	liver:	n/a	n/a
16	TAF1	chr18:9474790-9475698	SK-N-SH	brain:	n/a	n/a
17	MAX	chr18:9474467-9476144	ECC-1	luminal epithelium:	n/a	n/a
18	TEAD4	chr18:9474700-9475279	K562	blood:	n/a	n/a
19	MXI1	chr18:9474420-9476815	IMR90	lung:	n/a	n/a
20	IRF1	chr18:9474786-9475976	K562	blood:	n/a	chr18:9475839-9475853
21	POLR2A	chr18:9474715-9475363	A549	lung:	n/a	n/a
22	POLR2A	chr18:9474622-9475751	PANC-1	pancreas:	n/a	n/a
23	POLR2A	chr18:9474404-9476654	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chr18:9474405-9476216	HUVEC	blood vessel:	n/a	n/a
25	NR2F2	chr18:9475027-9475780	K562	blood:	n/a	n/a
26	TAF1	chr18:9474703-9475938	Hela-S3	cervix:	n/a	n/a
27	MAX	chr18:9474552-9476055	ECC-1	luminal epithelium:	n/a	n/a
28	MAZ	chr18:9474828-9475907	HepG2	liver:	n/a	n/a
29	SIX5	chr18:9475072-9475523	GM12878	blood:	n/a	chr18:9475312-9475326
30	CHD2	chr18:9474318-9476133	GM12878	blood:	n/a	chr18:9475475-9475485
31	POLR2A	chr18:9474554-9475867	HUVEC	blood vessel:	n/a	n/a
32	POLR2A	chr18:9474211-9476167	K562	blood:	n/a	n/a
33	E2F6	chr18:9474504-9476041	H1-hESC	embryonic stem cell:	n/a	chr18:9474970-9474980 chr18:9474832-9474841 chr18:9475753-9475764 chr18:9475759-9475768 chr18:9475295-9475304 chr18:9475214-9475223 chr18:9475754-9475766 chr18:9475491-9475500 chr18:9476023-9476033
34	ETS1	chr18:9475001-9475583	GM12878	blood:	n/a	chr18:9475312-9475325 chr18:9475376-9475389 chr18:9475375-9475388 chr18:9475068-9475081
35	ELF1	chr18:9475096-9475657	SK-N-SH	brain:	n/a	chr18:9475470-9475482
36	IRF1	chr18:9474958-9475665	K562	blood:	n/a	n/a
37	NFYB	chr18:9474891-9475525	K562	blood:	n/a	n/a
38	NFIC	chr18:9474771-9475494	ECC-1	luminal epithelium:	n/a	n/a
39	SRF	chr18:9475100-9475600	K562	blood:	n/a	n/a
40	EP300	chr18:9474507-9475898	ECC-1	luminal epithelium:	n/a	chr18:9475759-9475768
41	RFX5	chr18:9474749-9475829	Hela-S3	cervix:	n/a	chr18:9474820-9474828
42	KAP1	chr18:9475073-9475353	U2OS	brain:	n/a	n/a
43	POLR2A	chr18:9474908-9476160	NB4	blood:	n/a	n/a
44	SRF	chr18:9475099-9475612	H1-hESC	embryonic stem cell:	n/a	n/a
45	TAL1	chr18:9474718-9475727	K562	blood:	n/a	n/a
46	POLR2A	chr18:9474840-9476035	GM12891	blood:	n/a	n/a
47	POLR2A	chr18:9474526-9476143	HepG2	liver:	n/a	n/a
48	CTCF	chr18:9475000-9475150	GM12866	blood:	n/a	n/a
49	MAX	chr18:9474858-9476100	GM12878	blood:	n/a	n/a
50	POLR2A	chr18:9474710-9475997	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr18:9333428..9336571-chr18:9474335..9476989,6	MCF-7	breast:
2	chr18:9474922..9476536-chr18:9613527..9616238,2	MCF-7	breast:
3	chr18:9474439..9475367-chr5:180672929..180673983,3	Hela-S3	cervix:
4	chr18:9475085..9476082-chr8:26239931..26240578,2	Hela-S3	cervix:
5	chr1:149857548..149858376-chr18:9474738..9475411,2	Hela-S3	cervix:
6	chr18:9474867..9475442-chr5:40834265..40834948,2	Hela-S3	cervix:
7	chr1:104067956..104068800-chr18:9474823..9475445,2	Hela-S3	cervix:
8	chr18:9331992..9337338-chr18:9472584..9477624,6	MCF-7	breast:
9	chr18:9334546..9336965-chr18:9474025..9476757,3	K562	blood:
10	chr18:9474779..9475635-chr4:77069246..77070192,2	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000273335	TF binding region
RALBP1	TF binding region
ENSG00000184678	Chromatin interaction
ENSG00000104765	Chromatin interaction
ENSG00000154845	Chromatin interaction
ENSG00000264964	Chromatin interaction
ENSG00000145592	Chromatin interaction
ENSG00000224613	Chromatin interaction
ENSG00000233937	Chromatin interaction
ENSG00000128791	Chromatin interaction
ENSG00000263627	Chromatin interaction
ENSG00000185946	Chromatin interaction
ENSG00000228451	Chromatin interaction
ENSG00000138750	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11081480	0.85[ASW][hapmap];0.91[CEU][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.97[LWK][hapmap];0.89[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs167897	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2120318	0.85[ASW][hapmap];0.91[CEU][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs329016	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs384178	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs389066	0.91[CEU][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs426897	0.85[ASW][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.97[LWK][hapmap];0.92[MKK][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs449932	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs57315808	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs59365153	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60376740	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6506672	1.00[GIH][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6506673	0.82[CEU][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7232950	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7233044	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7235898	0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs7242756	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7245045	0.85[JPT][hapmap]
rs72936444	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]

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	nsv916373	chr18:9026803-9592201	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv1056407	chr18:9144345-9553764	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv1062025	chr18:9287249-9552470	Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv543643	chr18:9287249-9552470	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv833585	chr18:9401630-9597291	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv428005	chr18:9401658-9542396	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1049553	SPIRE1	cis	cerebellum	SCAN
rs1049553	GNAL	cis	cerebellum	SCAN
rs1049553	FAM38B	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:9474000-9476400	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr18:9474000-9476400	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr18:9474000-9477000	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr18:9474000-9477000	Active TSS	Right Ventricle	heart
5	chr18:9474200-9476400	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr18:9474200-9476400	Active TSS	Brain Anterior Caudate	brain
7	chr18:9474200-9476600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr18:9474200-9476600	Active TSS	Rectal Smooth Muscle	rectum
9	chr18:9474200-9476800	Active TSS	H9 Cell Line	embryonic stem cell
10	chr18:9474200-9476800	Active TSS	HUES48 Cell Line	embryonic stem cell
11	chr18:9474400-9475200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr18:9474400-9476400	Active TSS	Brain Substantia Nigra	brain
13	chr18:9474400-9476400	Active TSS	Left Ventricle	heart
14	chr18:9474400-9476400	Bivalent/Poised TSS	HepG2	liver
15	chr18:9474400-9476600	Active TSS	Aorta	Aorta
16	chr18:9474400-9476800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
17	chr18:9474400-9476800	Active TSS	Colonic Mucosa	Colon
18	chr18:9474400-9476800	Active TSS	Ovary	ovary
19	chr18:9474400-9477000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr18:9474600-9475200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
21	chr18:9474600-9475400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr18:9474600-9475600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr18:9474600-9475800	Active TSS	Primary hematopoietic stem cells	blood
24	chr18:9474600-9475800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
25	chr18:9474600-9475800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr18:9474600-9475800	Transcr. at gene 5' and 3'	Right Atrium	heart
27	chr18:9474600-9476000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
28	chr18:9474600-9476200	Active TSS	Primary T helper naive cells from peripheral blood	blood
29	chr18:9474600-9476200	Active TSS	Small Intestine	intestine
30	chr18:9474600-9476400	Active TSS	iPS-18 Cell Line	embryonic stem cell
31	chr18:9474600-9476400	Active TSS	Fetal Brain Male	brain
32	chr18:9474600-9476400	Active TSS	Fetal Lung	lung
33	chr18:9474600-9476400	Active TSS	Sigmoid Colon	Sigmoid Colon
34	chr18:9474600-9476600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr18:9474600-9476600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr18:9474600-9476600	Active TSS	Gastric	stomach
37	chr18:9474600-9476600	Active TSS	Placenta Amnion	Placenta Amnion
38	chr18:9474600-9476600	Active TSS	Stomach Mucosa	stomach
39	chr18:9474600-9476800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr18:9474600-9476800	Active TSS	Breast Myoepithelial Primary Cells	Breast
41	chr18:9474600-9476800	Active TSS	Psoas Muscle	Psoas
42	chr18:9474600-9477000	Active TSS	H1 Cell Line	embryonic stem cell
43	chr18:9474600-9477000	Active TSS	Esophagus	oesophagus
44	chr18:9474600-9477000	Active TSS	Fetal Kidney	kidney
45	chr18:9474600-9477000	Active TSS	NHDF-Ad	bronchial
46	chr18:9474600-9477200	Active TSS	Brain Germinal Matrix	brain
47	chr18:9474600-9477400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr18:9474800-9475200	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
49	chr18:9474800-9475200	Active TSS	Fetal Heart	heart
50	chr18:9474800-9475600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin

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