Variant report

Variant	rs55883912
Chromosome Location	chr5:1800046-1800047
allele	A/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	JUND	chr5:1799770-1802111	K562	blood:	n/a	chr5:1799990-1799999 chr5:1799987-1799996 chr5:1800154-1800168 chr5:1799991-1800000 chr5:1799988-1799997
2	RCOR1	chr5:1799791-1801796	Hela-S3	cervix:	n/a	n/a
3	CREB1	chr5:1799683-1800675	K562	blood:	n/a	n/a
4	FOXP2	chr5:1799615-1800136	PFSK-1	brain:	n/a	n/a
5	SMARCC2	chr5:1799899-1801839	Hela-S3	cervix:	n/a	n/a
6	MBD4	chr5:1799988-1800649	HepG2	liver:	n/a	n/a
7	CEBPB	chr5:1800023-1800057	HepG2	liver:	n/a	n/a
8	TAF1	chr5:1799562-1800203	HepG2	liver:	n/a	n/a
9	POLR2A	chr5:1799733-1800296	GM12891	blood:	n/a	n/a
10	TBP	chr5:1799280-1802309	K562	blood:	n/a	n/a
11	TAF1	chr5:1799658-1800317	ECC-1	luminal epithelium:	n/a	n/a
12	SIX5	chr5:1799803-1800138	K562	blood:	n/a	n/a
13	YY1	chr5:1799750-1800209	K562	blood:	n/a	chr5:1799972-1799991 chr5:1799980-1799988 chr5:1799967-1799989 chr5:1799984-1799993 chr5:1799987-1799996 chr5:1799979-1799989 chr5:1799977-1799989 chr5:1799985-1799996
14	CREB1	chr5:1799647-1800492	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr5:1799337-1802213	K562	blood:	n/a	n/a
16	POLR2A	chr5:1799035-1800569	GM12891	blood:	n/a	n/a
17	ATF3	chr5:1799868-1800064	GM12878	blood:	n/a	chr5:1799989-1800009
18	POLR2A	chr5:1799154-1802375	MCF10A-Er-Src	breast:	n/a	n/a
19	MAX	chr5:1799614-1800298	H1-hESC	embryonic stem cell:	n/a	chr5:1800000-1800009 chr5:1799998-1800011 chr5:1799988-1799998 chr5:1799999-1800010 chr5:1799985-1799995 chr5:1800000-1800009
20	MAX	chr5:1799413-1801875	HepG2	liver:	n/a	chr5:1800000-1800009 chr5:1800776-1800789 chr5:1799998-1800011 chr5:1800779-1800788 chr5:1799988-1799998 chr5:1800776-1800789 chr5:1799999-1800010 chr5:1799985-1799995 chr5:1800778-1800787 chr5:1800000-1800009 chr5:1800778-1800787 chr5:1800777-1800788 chr5:1800777-1800788 chr5:1800778-1800787
21	HA-E2F1	chr5:1799960-1802245	MCF-7	breast:	n/a	chr5:1801422-1801431 chr5:1801419-1801431 chr5:1801475-1801484 chr5:1800052-1800061 chr5:1801454-1801461 chr5:1801453-1801462 chr5:1799984-1799993
22	JUN	chr5:1799818-1800381	K562	blood:	n/a	chr5:1799990-1799999 chr5:1799987-1799996 chr5:1800154-1800168 chr5:1799991-1800000 chr5:1799988-1799997
23	TAL1	chr5:1799848-1800206	K562	blood:	n/a	n/a
24	USF1	chr5:1799632-1800288	K562	blood:	n/a	chr5:1799998-1800009
25	CCNT2	chr5:1799531-1800899	K562	blood:	n/a	chr5:1799739-1799748
26	CREB1	chr5:1799711-1800215	A549	lung:	n/a	n/a
27	ZKSCAN1	chr5:1799624-1800896	Hela-S3	cervix:	n/a	n/a
28	YY1	chr5:1799100-1800180	HepG2	liver:	n/a	chr5:1799972-1799991 chr5:1799980-1799988 chr5:1799967-1799989 chr5:1799984-1799993 chr5:1799987-1799996 chr5:1799979-1799989 chr5:1799977-1799989 chr5:1799985-1799996
29	E2F6	chr5:1799778-1800180	K562	blood:	n/a	chr5:1800052-1800061 chr5:1799984-1799993
30	REST	chr5:1799742-1800296	PFSK-1	brain:	n/a	n/a
31	CHD1	chr5:1799337-1802013	GM12878	blood:	n/a	chr5:1801420-1801430
32	POLR2A	chr5:1799365-1800786	K562	blood:	n/a	n/a
33	STAT5A	chr5:1800000-1800304	GM12878	blood:	n/a	n/a
34	CTCF	chr5:1799945-1800701	GM12878	blood:	n/a	n/a
35	EP300	chr5:1799793-1800437	GM12878	blood:	n/a	chr5:1800073-1800086 chr5:1800283-1800293
36	TBP	chr5:1799787-1802268	H1-hESC	embryonic stem cell:	n/a	n/a
37	RCOR1	chr5:1799815-1800927	K562	blood:	n/a	n/a
38	POLR2A	chr5:1799089-1802204	HepG2	liver:	n/a	n/a
39	USF1	chr5:1799727-1800276	A549	lung:	n/a	chr5:1799998-1800009
40	POLR2A	chr5:1799582-1801049	ECC-1	luminal epithelium:	n/a	n/a
41	TEAD4	chr5:1799783-1801813	K562	blood:	n/a	n/a
42	POLR2A	chr5:1799155-1802340	Hela-S3	cervix:	n/a	n/a
43	MYC	chr5:1799838-1800089	HepG2	liver:	n/a	chr5:1800000-1800009 chr5:1799998-1800011 chr5:1799988-1799998 chr5:1799999-1800010 chr5:1799985-1799995 chr5:1800000-1800009
44	POLR2A	chr5:1799718-1800332	GM12892	blood:	n/a	n/a
45	FOXA2	chr5:1799968-1800440	HepG2	liver:	n/a	n/a
46	TAF1	chr5:1799614-1800388	A549	lung:	n/a	n/a
47	POLR2A	chr5:1798976-1802439	Hela-S3	cervix:	n/a	n/a
48	POLR2A	chr5:1799636-1800406	PANC-1	pancreas:	n/a	n/a
49	YY1	chr5:1799603-1800319	ECC-1	luminal epithelium:	n/a	chr5:1799972-1799991 chr5:1799980-1799988 chr5:1799967-1799989 chr5:1799984-1799993 chr5:1799987-1799996 chr5:1799979-1799989 chr5:1799977-1799989 chr5:1799985-1799996
50	TFAP2C	chr5:1799840-1802225	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:56707453..56709236-chr5:1799018..1801500,2	MCF-7	breast:
2	chr11:10830116..10831217-chr5:1799336..1800336,3	Hela-S3	cervix:
3	chr5:1799841..1802509-chr5:1881368..1882987,2	K562	blood:
4	chr12:46777055..46777768-chr5:1799635..1800155,2	Hela-S3	cervix:
5	chr5:1799569..1802884-chr5:1886598..1889173,4	MCF-7	breast:
6	chr5:1799911..1800807-chr9:106856184..106857050,2	Hela-S3	cervix:
7	chr17:73716503..73719364-chr5:1799934..1802626,2	MCF-7	breast:
8	chr5:1793765..1806799-chr5:1879445..1889322,45	MCF-7	breast:
9	chr5:1344287..1345865-chr5:1799704..1802609,2	K562	blood:
10	chr5:1796457..1805482-chr5:1878036..1885786,21	MCF-7	breast:
11	chr5:1343974..1345787-chr5:1800029..1802609,2	K562	blood:
12	chr5:1798942..1801341-chr5:1879541..1882987,3	K562	blood:
13	chr15:34729318..34730097-chr5:1799590..1800354,2	Hela-S3	cervix:
14	chr2:197791233..197791932-chr5:1799906..1800564,2	HCT-116	colon:
15	chr5:1799532..1800526-chrX:15693324..15693931,2	Hela-S3	cervix:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NDUFS6-9	chr5:1799992-1801417	NONHSAT100069

Variant related genes	Relation type
MRPL36	TF binding region
NDUFS6	TF binding region
ENSG00000249326	Chromatin interaction
ENSG00000049656	Chromatin interaction
ENSG00000136824	Chromatin interaction
ENSG00000110321	Chromatin interaction
ENSG00000246308	Chromatin interaction
ENSG00000257261	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000175265	Chromatin interaction
ENSG00000249116	Chromatin interaction
ENSG00000197121	Chromatin interaction
ENSG00000113430	Chromatin interaction
ENSG00000186312	Chromatin interaction
ENSG00000132470	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11133910	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11133911	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11133912	0.93[ASN][1000 genomes]
rs13187162	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1845288	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1873926	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2242412	0.87[ASN][1000 genomes]
rs2276986	0.97[ASN][1000 genomes]
rs2291944	0.98[ASN][1000 genomes]
rs34233926	0.95[ASN][1000 genomes]
rs35380881	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3756343	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3756345	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3756346	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3776141	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3776142	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3776143	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3776144	0.96[ASN][1000 genomes]
rs3776145	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3776146	0.95[ASN][1000 genomes]
rs3776149	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3822364	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4147769	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4147770	0.98[ASN][1000 genomes]
rs4147772	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4147773	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4975845	0.84[ASN][1000 genomes]
rs4975848	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4975849	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4975851	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4975852	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4975853	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6555012	0.92[ASN][1000 genomes]
rs6863367	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7702843	0.92[ASN][1000 genomes]
rs972890	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs972891	0.98[ASN][1000 genomes]
rs972892	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs974722	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933805	chr5:1450724-1941619	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv817407	chr5:1495354-2191460	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	107 gene(s)	inside rSNPs	diseases
3	nsv1034552	chr5:1658338-1856553	Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	44 gene(s)	inside rSNPs	diseases
4	nsv537606	chr5:1658338-1856553	Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	44 gene(s)	inside rSNPs	diseases
5	nsv1033147	chr5:1717303-1815821	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
6	nsv869236	chr5:1719263-2259100	Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
7	nsv1020703	chr5:1724199-1814288	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
8	nsv537608	chr5:1724199-1814288	Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
9	nsv1024133	chr5:1736691-1826510	Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
10	nsv537609	chr5:1736691-1826510	Genic enhancers Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:1791000-1800200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr5:1798400-1802400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr5:1798800-1800600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr5:1798800-1800600	Active TSS	Primary T helper cells PMA-I stimulated	--
5	chr5:1798800-1802200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr5:1798800-1802400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr5:1798800-1802800	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr5:1799000-1800200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
9	chr5:1799000-1800400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr5:1799000-1802200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr5:1799000-1802200	Active TSS	Left Ventricle	heart
12	chr5:1799000-1802400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr5:1799000-1802400	Active TSS	H9 Cell Line	embryonic stem cell
14	chr5:1799000-1802400	Active TSS	Psoas Muscle	Psoas
15	chr5:1799000-1802600	Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr5:1799000-1802600	Active TSS	iPS-20b Cell Line	embryonic stem cell
17	chr5:1799000-1802600	Active TSS	Fetal Intestine Small	intestine
18	chr5:1799000-1802600	Active TSS	A549	lung
19	chr5:1799200-1800200	Active TSS	Breast Myoepithelial Primary Cells	Breast
20	chr5:1799200-1800200	Active TSS	Fetal Lung	lung
21	chr5:1799200-1800200	Active TSS	HMEC	breast
22	chr5:1799200-1800200	Active TSS	NHEK	skin
23	chr5:1799200-1800600	Active TSS	Primary T helper naive cells from peripheral blood	blood
24	chr5:1799200-1800600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr5:1799200-1800600	Active TSS	Fetal Intestine Large	intestine
26	chr5:1799200-1800600	Active TSS	HSMM	muscle
27	chr5:1799200-1800800	Active TSS	K562	blood
28	chr5:1799200-1801400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr5:1799200-1802200	Active TSS	iPS-15b Cell Line	embryonic stem cell
30	chr5:1799200-1802200	Active TSS	iPS-18 Cell Line	embryonic stem cell
31	chr5:1799200-1802200	Active TSS	Aorta	Aorta
32	chr5:1799200-1802200	Active TSS	Fetal Kidney	kidney
33	chr5:1799200-1802200	Active TSS	Sigmoid Colon	Sigmoid Colon
34	chr5:1799200-1802200	Active TSS	Small Intestine	intestine
35	chr5:1799200-1802200	Active TSS	NHDF-Ad	bronchial
36	chr5:1799200-1802400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr5:1799200-1802600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr5:1799200-1802600	Active TSS	Pancreatic Islets	Pancreatic Islet
39	chr5:1799200-1802800	Active TSS	GM12878-XiMat	blood
40	chr5:1799400-1800200	Active TSS	Primary T cells from cord blood	blood
41	chr5:1799400-1800200	Active TSS	Primary hematopoietic stem cells short term culture	blood
42	chr5:1799400-1800200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
43	chr5:1799400-1800200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr5:1799400-1800200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr5:1799400-1800200	Active TSS	Muscle Satellite Cultured Cells	--
46	chr5:1799400-1800200	Active TSS	Rectal Mucosa Donor 29	rectum
47	chr5:1799400-1800200	Active TSS	Rectal Mucosa Donor 31	rectum
48	chr5:1799400-1800200	Active TSS	Skeletal Muscle Male	skeletal muscle
49	chr5:1799400-1800200	Active TSS	Monocytes-CD14+_RO01746	blood
50	chr5:1799400-1800200	Active TSS	NH-A	brain

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