Variant report

Variant	rs480498
Chromosome Location	chr1:179853096-179853097
allele	C/G
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	STAT3	chr1:179852817-179853196	MCF10A-Er-Src	breast:	n/a	chr1:179852957-179852969 chr1:179852953-179852965
2	POLR2A	chr1:179850924-179853177	GM15510	blood:	n/a	n/a
3	CREB1	chr1:179852829-179853323	HepG2	liver:	n/a	n/a
4	STAT5A	chr1:179851010-179853159	GM12878	blood:	n/a	chr1:179852957-179852969 chr1:179852341-179852353 chr1:179851189-179851212 chr1:179851147-179851158 chr1:179852288-179852300 chr1:179852953-179852965
5	FOS	chr1:179852704-179853292	MCF10A-Er-Src	breast:	n/a	chr1:179852958-179852967 chr1:179853052-179853060 chr1:179852986-179852994 chr1:179852982-179852993
6	CCNT2	chr1:179852773-179853105	K562	blood:	n/a	n/a
7	ATF2	chr1:179852414-179853231	GM12878	blood:	n/a	n/a
8	POLR2A	chr1:179852940-179853190	Hela-S3	cervix:	n/a	n/a
9	RUNX3	chr1:179852834-179853276	GM12878	blood:	n/a	n/a
10	POLR2A	chr1:179850841-179853186	GM12892	blood:	n/a	n/a
11	WRNIP1	chr1:179851025-179853188	GM12878	blood:	n/a	n/a
12	MAZ	chr1:179850829-179853104	K562	blood:	n/a	n/a
13	POLR2A	chr1:179852951-179853181	ProgFib	skin:	n/a	n/a
14	BATF	chr1:179852838-179853186	GM12878	blood:	n/a	chr1:179853000-179853008
15	POLR2A	chr1:179852868-179853294	GM12891	blood:	n/a	n/a
16	ATF2	chr1:179852432-179853269	GM12878	blood:	n/a	n/a
17	NFYB	chr1:179852977-179853230	K562	blood:	n/a	n/a
18	JUN	chr1:179850203-179853448	K562	blood:	n/a	chr1:179852958-179852967 chr1:179853052-179853060 chr1:179852986-179852994 chr1:179852982-179852993
19	POLR2A	chr1:179851009-179853215	GM19193	blood:	n/a	n/a
20	POLR2A	chr1:179850606-179853325	GM12878	blood:	n/a	n/a
21	POU2F2	chr1:179852908-179853198	GM12891	blood:	n/a	n/a
22	CREB1	chr1:179852766-179853302	HepG2	liver:	n/a	n/a
23	CREB1	chr1:179850960-179853337	GM12878	blood:	n/a	n/a
24	CHD1	chr1:179850810-179853436	IMR90	lung:	n/a	n/a
25	RUNX3	chr1:179851151-179853342	GM12878	blood:	n/a	n/a
26	JUN	chr1:179853063-179853102	HepG2	liver:	n/a	n/a
27	POLR2A	chr1:179850422-179853318	GM12878	blood:	n/a	n/a
28	POLR2A	chr1:179852810-179853267	GM12892	blood:	n/a	n/a
29	RELA	chr1:179850808-179853193	GM15510	blood:	n/a	n/a
30	TBL1XR1	chr1:179852904-179853233	K562	blood:	n/a	n/a
31	JUND	chr1:179852581-179853212	K562	blood:	n/a	chr1:179852958-179852967 chr1:179853052-179853060 chr1:179853050-179853061 chr1:179852986-179852994 chr1:179852982-179852993
32	CHD1	chr1:179850646-179853274	GM12878	blood:	n/a	n/a
33	MYC	chr1:179852862-179853294	MCF10A-Er-Src	breast:	n/a	n/a
34	EBF1	chr1:179853022-179853183	GM12878	blood:	n/a	n/a
35	POLR2A	chr1:179850387-179853379	MCF10A-Er-Src	breast:	n/a	n/a
36	POLR2A	chr1:179852836-179853230	GM12891	blood:	n/a	n/a
37	RCOR1	chr1:179850779-179853101	Hela-S3	cervix:	n/a	n/a
38	POLR2A	chr1:179850786-179853263	GM18505	blood:	n/a	n/a
39	FOS	chr1:179852739-179853261	MCF10A-Er-Src	breast:	n/a	chr1:179852958-179852967 chr1:179853052-179853060 chr1:179852986-179852994 chr1:179852982-179852993
40	FOS	chr1:179852811-179853222	MCF10A-Er-Src	breast:	n/a	chr1:179852958-179852967 chr1:179853052-179853060 chr1:179852986-179852994 chr1:179852982-179852993
41	RELA	chr1:179850992-179853185	GM18951	blood:	n/a	n/a
42	POLR2A	chr1:179850804-179853259	GM12891	blood:	n/a	n/a
43	PAX5	chr1:179852944-179853161	GM12878	blood:	n/a	n/a
44	MTA3	chr1:179850687-179853274	GM12878	blood:	n/a	n/a
45	POLR2A	chr1:179850786-179853219	GM19099	blood:	n/a	n/a
46	POLR2A	chr1:179850381-179853322	GM12891	blood:	n/a	n/a
47	USF2	chr1:179852475-179853146	Hela-S3	cervix:	n/a	n/a
48	CREB1	chr1:179852708-179853396	K562	blood:	n/a	n/a
49	FOS	chr1:179852648-179853222	MCF10A-Er-Src	breast:	n/a	chr1:179852958-179852967 chr1:179853052-179853060 chr1:179852986-179852994 chr1:179852982-179852993
50	POLR2A	chr1:179852916-179853192	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:179848142..179854405-chr1:179919774..179927189,17	MCF-7	breast:
2	chr1:179833317..179835863-chr1:179849395..179853272,4	MCF-7	breast:
3	chr1:179851639..179853343-chr1:181059453..181061374,2	K562	blood:
4	chr1:179849896..179853295-chr1:179868800..179873439,8	K562	blood:
5	chr1:179849016..179853452-chr1:179922333..179928502,16	K562	blood:
6	chr1:179851750..179853316-chr1:179871986..179873575,2	MCF-7	breast:
7	chr1:179850058..179853356-chr1:179869131..179876291,8	K562	blood:
8	chr1:179847679..179853408-chr1:179922379..179926886,15	MCF-7	breast:
9	chr1:179844528..179853403-chr1:179920065..179927793,25	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CEP350-3	chr1:179853072-179853163	NONHSAT008226

Variant related genes	Relation type
ENSG00000272906	TF binding region
TOR1AIP1	TF binding region
ENSG00000135837	Chromatin interaction
ENSG00000143337	Chromatin interaction
ENSG00000264916	Chromatin interaction
ENSG00000272198	Chromatin interaction
ENSG00000258664	Chromatin interaction
ENSG00000260360	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1014394	0.88[EUR][1000 genomes]
rs1144575	0.95[ASN][1000 genomes]
rs1148812	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1148815	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1148817	0.87[EUR][1000 genomes]
rs12062341	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12062383	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1281378	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1281408	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1281411	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1281412	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1281413	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1281428	0.93[ASN][1000 genomes]
rs1281429	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1281430	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1281432	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1298477	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1298479	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1300068	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2007148	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2245425	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2249346	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2762858	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2777908	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2777909	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2777917	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2794582	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2794583	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs474258	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs475233	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs475434	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs479094	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs480377	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs486906	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs501300	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs502036	0.83[EUR][1000 genomes]
rs505789	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs505837	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs507603	0.92[ASN][1000 genomes]
rs514421	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs518774	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs522534	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs530369	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs530854	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs538512	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs547776	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs549650	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs553830	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs555270	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs555526	0.93[ASN][1000 genomes]
rs589780	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs599185	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs600046	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs600553	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs605807	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs609521	0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs612215	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs615337	0.81[EUR][1000 genomes]
rs644412	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7530362	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005808	chr1:179783922-179864710	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv1005051	chr1:179785643-179861950	Flanking Active TSS Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
3	nsv429936	chr1:179790343-180214343	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
4	nsv429947	chr1:179790518-179925104	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	esv1815608	chr1:179813499-180067988	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
6	nsv429958	chr1:179814306-179994628	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
7	nsv518936	chr1:179847402-179858333	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179849400-179853400	Active TSS	K562	blood
2	chr1:179849800-179853200	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr1:179850200-179853200	Active TSS	NHEK	skin
4	chr1:179850200-179853600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr1:179850200-179853600	Active TSS	HMEC	breast
6	chr1:179850400-179853400	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr1:179850400-179853400	Active TSS	Right Ventricle	heart
8	chr1:179850400-179853400	Active TSS	NHDF-Ad	bronchial
9	chr1:179850400-179853600	Active TSS	Aorta	Aorta
10	chr1:179850400-179853800	Active TSS	NHLF	lung
11	chr1:179850600-179853200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr1:179850600-179853200	Active TSS	iPS-15b Cell Line	embryonic stem cell
13	chr1:179850600-179853200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
14	chr1:179850600-179853200	Active TSS	Fetal Intestine Small	intestine
15	chr1:179850600-179853400	Active TSS	H1 Cell Line	embryonic stem cell
16	chr1:179850600-179853400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr1:179850600-179853400	Active TSS	Duodenum Smooth Muscle	Duodenum
18	chr1:179850600-179853400	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr1:179850600-179853600	Active TSS	iPS-20b Cell Line	embryonic stem cell
20	chr1:179850600-179853600	Active TSS	Breast Myoepithelial Primary Cells	Breast
21	chr1:179850600-179853600	Active TSS	Colon Smooth Muscle	Colon
22	chr1:179850600-179853800	Active TSS	Fetal Intestine Large	intestine
23	chr1:179850800-179853200	Active TSS	H9 Cell Line	embryonic stem cell
24	chr1:179850800-179853200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr1:179850800-179853200	Active TSS	Thymus	Thymus
26	chr1:179850800-179853400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
27	chr1:179850800-179853600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr1:179850800-179853600	Active TSS	HUES64 Cell Line	embryonic stem cell
29	chr1:179850800-179854200	Active TSS	GM12878-XiMat	blood
30	chr1:179851000-179853200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr1:179851000-179853200	Active TSS	Gastric	stomach
32	chr1:179851200-179853200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
33	chr1:179851200-179853200	Active TSS	Primary T helper naive cells from peripheral blood	blood
34	chr1:179852000-179853200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
35	chr1:179852200-179853400	Flanking Active TSS	Adipose Nuclei	Adipose
36	chr1:179852200-179853400	Active TSS	Right Atrium	heart
37	chr1:179852400-179853200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
38	chr1:179852400-179853200	Flanking Active TSS	Placenta	Placenta
39	chr1:179852400-179853200	Flanking Active TSS	Rectal Smooth Muscle	rectum
40	chr1:179852400-179853400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr1:179852400-179853400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr1:179852400-179853600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
43	chr1:179852400-179853600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr1:179852600-179853200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
45	chr1:179852600-179853200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
46	chr1:179852600-179853200	Flanking Active TSS	Primary B cells from peripheral blood	blood
47	chr1:179852600-179853200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
48	chr1:179852600-179853200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
49	chr1:179852600-179853200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
50	chr1:179852600-179853200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain

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