Variant report

Variant	rs74124647
Chromosome Location	chr1:161102882-161102883
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	TCF7L2	chr1:161102414-161103067	PANC-1	pancreas:	n/a	n/a
2	GABPA	chr1:161102061-161103054	K562	blood:	n/a	chr1:161102472-161102481
3	CTCF	chr1:161102512-161103013	K562	blood:	n/a	chr1:161102763-161102776
4	USF1	chr1:161102626-161103144	A549	lung:	n/a	n/a
5	POLR2A	chr1:161102074-161103121	A549	lung:	n/a	n/a
6	CEBPB	chr1:161102412-161103062	A549	lung:	n/a	n/a
7	YY1	chr1:161101629-161103266	H1-hESC	embryonic stem cell:	n/a	chr1:161102356-161102376 chr1:161102327-161102336 chr1:161102644-161102663 chr1:161102649-161102657 chr1:161102809-161102831 chr1:161102643-161102663 chr1:161102167-161102178 chr1:161102472-161102486 chr1:161102646-161102668 chr1:161103062-161103073
8	POLR2A	chr1:161102034-161103161	K562	blood:	n/a	n/a
9	ETS1	chr1:161102362-161102982	A549	lung:	n/a	n/a
10	POLR2A	chr1:161101790-161103756	H1-neurons	neurons:	n/a	n/a
11	SIN3AK20	chr1:161102061-161103134	SK-N-SH	brain:	n/a	n/a
12	JUND	chr1:161102483-161103030	A549	lung:	n/a	chr1:161102813-161102824 chr1:161102815-161102824 chr1:161102815-161102823 chr1:161102815-161102822
13	POLR2A	chr1:161102206-161103259	HCT-116	colon:	n/a	n/a
14	EP300	chr1:161102374-161103180	A549	lung:	n/a	chr1:161102815-161102824
15	PML	chr1:161101883-161103290	GM12878	blood:	n/a	n/a
16	CTCF	chr1:161102840-161102990	SK-N-SH_RA	brain:	n/a	n/a
17	MAX	chr1:161101816-161102999	GM12878	blood:	n/a	chr1:161102472-161102482 chr1:161102814-161102823 chr1:161101821-161101831
18	EBF1	chr1:161102545-161103209	GM12878	blood:	n/a	n/a
19	ZNF143	chr1:161102452-161103058	Hela-S3	cervix:	n/a	chr1:161102472-161102482 chr1:161102497-161102515
20	NR3C1	chr1:161101996-161102905	A549	lung:	n/a	chr1:161102462-161102475 chr1:161102305-161102318 chr1:161102646-161102660
21	JUN	chr1:161101851-161103971	K562	blood:	n/a	chr1:161102815-161102824 chr1:161102471-161102480 chr1:161102815-161102823 chr1:161102815-161102822
22	POLR2A	chr1:161101946-161103694	MCF10A-Er-Src	breast:	n/a	n/a
23	KAP1	chr1:161102460-161103554	U2OS	brain:	n/a	n/a
24	BCLAF1	chr1:161102208-161103212	GM12878	blood:	n/a	chr1:161102815-161102824 chr1:161102814-161102823
25	NFIC	chr1:161102397-161102895	HepG2	liver:	n/a	n/a
26	MAZ	chr1:161101721-161103128	HepG2	liver:	n/a	chr1:161102472-161102482 chr1:161102814-161102823 chr1:161101821-161101831
27	SP1	chr1:161101912-161103401	A549	lung:	n/a	chr1:161102458-161102467 chr1:161102083-161102092 chr1:161103062-161103071 chr1:161102116-161102130 chr1:161102082-161102094 chr1:161102471-161102483 chr1:161102019-161102033 chr1:161102169-161102178
28	POLR2A	chr1:161101946-161103202	ECC-1	luminal epithelium:	n/a	n/a
29	POLR2A	chr1:161101652-161103366	HUVEC	blood vessel:	n/a	n/a
30	POLR2A	chr1:161102173-161103614	MCF10A-Er-Src	breast:	n/a	n/a
31	CTCF	chr1:161102740-161102890	Hela-S3	cervix:	n/a	chr1:161102763-161102776
32	POLR2A	chr1:161101750-161103222	HL-60	blood:	n/a	n/a
33	GABPA	chr1:161102416-161103165	Hela-S3	cervix:	n/a	chr1:161102472-161102481
34	NR2F2	chr1:161102448-161103126	K562	blood:	n/a	n/a
35	POLR2A	chr1:161101883-161103399	H1-hESC	embryonic stem cell:	n/a	n/a
36	CTCF	chr1:161102550-161102933	GM12878	blood:	n/a	chr1:161102763-161102776
37	YY1	chr1:161102053-161103128	K562	blood:	n/a	chr1:161102356-161102376 chr1:161102327-161102336 chr1:161102644-161102663 chr1:161102649-161102657 chr1:161102809-161102831 chr1:161102643-161102663 chr1:161102167-161102178 chr1:161102472-161102486 chr1:161102646-161102668 chr1:161103062-161103073
38	GATA3	chr1:161102427-161103155	T-47D	breast:	n/a	n/a
39	STAT5A	chr1:161101798-161103299	GM12878	blood:	n/a	chr1:161102815-161102824 chr1:161102814-161102823 chr1:161101970-161101982
40	GABPA	chr1:161102319-161103426	A549	lung:	n/a	chr1:161102472-161102481
41	SMC3	chr1:161102685-161102891	GM12878	blood:	n/a	chr1:161102770-161102777
42	IRF1	chr1:161102180-161103075	K562	blood:	n/a	chr1:161102815-161102824
43	GABPA	chr1:161102266-161103114	HepG2	liver:	n/a	chr1:161102472-161102481
44	GTF2F1	chr1:161102434-161103337	Hela-S3	cervix:	n/a	n/a
45	MXI1	chr1:161101989-161103340	HepG2	liver:	n/a	n/a
46	POLR2A	chr1:161102208-161102977	GM10847	blood:	n/a	n/a
47	YY1	chr1:161101943-161103188	GM12878	blood:	n/a	chr1:161102356-161102376 chr1:161102327-161102336 chr1:161102644-161102663 chr1:161102649-161102657 chr1:161102809-161102831 chr1:161102643-161102663 chr1:161102167-161102178 chr1:161102472-161102486 chr1:161102646-161102668 chr1:161103062-161103073
48	CTCF	chr1:161102780-161102930	RPTEC	kidney:	n/a	n/a
49	TBP	chr1:161102198-161103058	H1-hESC	embryonic stem cell:	n/a	n/a
50	REST	chr1:161102365-161103302	A549	lung:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:161102858-161102908	T-47D	breast:	n/a
2	chr1:161102858-161102908	HCT-116	colon:	n/a
3	chr1:161102858-161102908	LNCaP	prostate:	n/a
4	chr1:161102858-161102908	SAEC	small airway:	n/a
5	chr1:161102858-161102908	GM19239	blood:	n/a
6	chr1:161102858-161102908	SK-N-SH	brain:	n/a
7	chr1:161102858-161102908	MCF10A-Er-Src	breast:	n/a
8	chr1:161102858-161102908	SK-N-SH_RA	brain:	n/a
9	chr1:161102858-161102908	RPTEC	kidney:	n/a
10	chr1:161102858-161102908	HCPEpiC	choroid plexus:	n/a
11	chr1:161102858-161102908	SKMC	muscle:	n/a
12	chr1:161102858-161102908	BJ	skin:	n/a
13	chr1:161102858-161102908	NHBE	bronchial:	n/a
14	chr1:161102858-161102908	HPAEpiC	pulmonary alveolar:	n/a
15	chr1:161102858-161102908	IMR90	lung:	fetal
16	chr1:161102858-161102908	NB4	blood:	n/a
17	chr1:161102858-161102908	HEK293	kidney:	embryo
18	chr1:161102858-161102908	AG09319	gingival:	n/a
19	chr1:161102858-161102908	AoSMC	blood vessel:	n/a
20	chr1:161102858-161102908	U87	brain:	n/a
21	chr1:161102858-161102908	NH-A	brain:	n/a
22	chr1:161102858-161102908	SK-N-MC	brain:	n/a
23	chr1:161102858-161102908	K562	blood:	n/a
24	chr1:161102858-161102908	ProgFib	skin:	n/a
25	chr1:161102858-161102908	HUVEC	blood vessel:	n/a
26	chr1:161102858-161102908	HRPEpiC	eye:	n/a
27	chr1:161102858-161102908	MCF-7	breast:	n/a
28	chr1:161102858-161102908	NT2-D1	testis:	n/a
29	chr1:161102858-161102908	GM12892	blood:	n/a
30	chr1:161102858-161102908	HMEC	breast:	n/a
31	chr1:161102858-161102908	GM06990	blood:	n/a
32	chr1:161102858-161102908	HRE	kidney:	n/a
33	chr1:161102858-161102908	HL-60	blood:	n/a
34	chr1:161102858-161102908	BE2_C	brain:	n/a
35	chr1:161102858-161102908	HCM	heart:	n/a
36	chr1:161102858-161102908	HCF	heart:	n/a
37	chr1:161102858-161102908	Caco-2	colon:	n/a
38	chr1:161102858-161102908	HEEpiC	esophagus:	n/a
39	chr1:161102858-161102908	AG04449	skin:	fetal
40	chr1:161102858-161102908	HAEpiC	amniotic membrane:	n/a
41	chr1:161102858-161102908	Hepatocyte	liver:	n/a
42	chr1:161102858-161102908	Hela-S3	cervix:	n/a
43	chr1:161102858-161102908	HRCEpiC	kidney:	n/a
44	chr1:161102858-161102908	A549	lung:	n/a
45	chr1:161102858-161102908	AG04450	lung:	fetal
46	chr1:161102858-161102908	HIPEpiC	eye:	n/a
47	chr1:161102858-161102908	H1-hESC	embryonic stem cell:	embryo
48	chr1:161102858-161102908	PrEC	prostate:	n/a
49	chr1:161102858-161102908	HNPCEpiC	eye:	n/a
50	chr1:161102858-161102908	HepG2	liver:	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:161014566..161017528-chr1:161100154..161103523,4	K562	blood:
2	chr1:161007064..161010778-chr1:161101040..161104167,3	MCF-7	breast:
3	chr1:161101282..161104235-chr1:161127986..161130833,4	MCF-7	breast:
4	chr1:161102335..161103056-chr15:67358037..67358574,2	Hela-S3	cervix:
5	chr1:161101050..161105947-chr1:161126092..161130683,11	K562	blood:
6	chr1:161100691..161104235-chr1:161128857..161130819,4	K562	blood:
7	chr1:161066559..161072259-chr1:161099379..161104380,9	MCF-7	breast:
8	chr1:161100611..161104525-chr1:161121984..161125219,4	MCF-7	breast:
9	chr1:161015658..161017550-chr1:161101051..161103879,2	K562	blood:
10	chr1:161015399..161016324-chr1:161102283..161103079,2	MCF-7	breast:
11	chr1:161102011..161102885-chr2:75937631..75938150,2	Hela-S3	cervix:
12	chr1:161100609..161105995-chr1:161120333..161125390,9	MCF-7	breast:
13	chr1:161100027..161103465-chr1:161134887..161137955,5	K562	blood:
14	chr1:161101013..161103871-chr1:161121699..161125704,9	K562	blood:
15	chr1:161013542..161018278-chr1:161100825..161104206,7	MCF-7	breast:
16	chr1:160987861..160992104-chr1:161101436..161104060,5	K562	blood:
17	chr1:161067686..161069382-chr1:161100997..161103060,2	K562	blood:
18	chr1:161102780..161103398-chr1:161128647..161129222,2	MCF-7	breast:
19	chr1:161102178..161105120-chr1:161145424..161148763,5	K562	blood:
20	chr1:161100027..161102916-chr1:161132751..161137101,5	K562	blood:
21	chr1:161102178..161105120-chr1:161145424..161148763,3	K562	blood:
22	chr1:161102076..161102885-chr15:93425741..93426245,2	Hela-S3	cervix:
23	chr1:160989106..160992104-chr1:161101728..161103686,4	K562	blood:
24	chr1:161102526..161103311-chr5:126113505..126114227,2	Hela-S3	cervix:
25	chr1:161099668..161103758-chr1:161134918..161138367,5	MCF-7	breast:
26	chr1:160989601..160993379-chr1:161101301..161104263,5	MCF-7	breast:
27	chr1:161101281..161106554-chr1:161121720..161125014,7	K562	blood:
28	chr1:161102096..161102901-chr17:39844857..39845536,3	Hela-S3	cervix:
29	chr1:161102266..161103265-chr7:55433401..55434033,2	Hela-S3	cervix:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NIT1-1	chr1:161102480-161106264	NONHSAT007118
2	lnc-NIT1-1	chr1:161102698-161103202	NONHSAT007119

Variant related genes	Relation type
DEDD	TF binding region
DEDD	CpG island
ENSG00000272888	Chromatin interaction
ENSG00000270149	Chromatin interaction
ENSG00000158773	Chromatin interaction
ENSG00000215845	Chromatin interaction
ENSG00000143258	Chromatin interaction
ENSG00000173812	Chromatin interaction
ENSG00000158769	Chromatin interaction
ENSG00000162755	Chromatin interaction
ENSG00000132434	Chromatin interaction
ENSG00000224985	Chromatin interaction
ENSG00000005436	Chromatin interaction
ENSG00000166949	Chromatin interaction
ENSG00000143224	Chromatin interaction
ENSG00000158850	Chromatin interaction
ENSG00000143222	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs55675252	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57560345	0.84[AFR][1000 genomes]
rs61642842	1.00[AFR][1000 genomes]
rs74124633	1.00[AMR][1000 genomes]
rs74124643	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74124646	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74124650	1.00[AFR][1000 genomes]
rs74124653	1.00[AFR][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	nsv530077	chr1:160836448-161284904	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 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	chr1:161100400-161103400	Active TSS	Psoas Muscle	Psoas
2	chr1:161100600-161103400	Active TSS	GM12878-XiMat	blood
3	chr1:161100600-161104400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr1:161100800-161103800	Active TSS	NHLF	lung
5	chr1:161100800-161104000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr1:161100800-161104000	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr1:161100800-161104000	Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr1:161100800-161104200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr1:161101000-161103200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:161101000-161103400	Active TSS	Right Ventricle	heart
11	chr1:161101000-161103800	Active TSS	Aorta	Aorta
12	chr1:161101000-161104000	Active TSS	H1 Cell Line	embryonic stem cell
13	chr1:161101000-161104000	Active TSS	H9 Cell Line	embryonic stem cell
14	chr1:161101000-161104000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr1:161101000-161104000	Active TSS	HSMM	muscle
16	chr1:161101200-161103400	Active TSS	HUES48 Cell Line	embryonic stem cell
17	chr1:161101200-161103600	Active TSS	Fetal Muscle Trunk	muscle
18	chr1:161101200-161103800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr1:161101200-161103800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:161101200-161103800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr1:161101200-161103800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr1:161101200-161103800	Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr1:161101200-161104000	Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr1:161101200-161104000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr1:161101200-161104000	Active TSS	HUES6 Cell Line	embryonic stem cell
26	chr1:161101200-161104000	Active TSS	HUES64 Cell Line	embryonic stem cell
27	chr1:161101200-161104000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr1:161101200-161104200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr1:161101400-161103200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr1:161101400-161103200	Active TSS	Brain Substantia Nigra	brain
31	chr1:161101400-161103200	Active TSS	Fetal Lung	lung
32	chr1:161101400-161103200	Active TSS	Lung	lung
33	chr1:161101400-161103400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr1:161101400-161103400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr1:161101400-161103400	Active TSS	Muscle Satellite Cultured Cells	--
36	chr1:161101400-161103400	Active TSS	Fetal Stomach	stomach
37	chr1:161101400-161103400	Active TSS	Left Ventricle	heart
38	chr1:161101400-161103400	Active TSS	HSMMtube	muscle
39	chr1:161101400-161103400	Active TSS	NH-A	brain
40	chr1:161101400-161103600	Active TSS	Duodenum Smooth Muscle	Duodenum
41	chr1:161101400-161103600	Active TSS	Fetal Kidney	kidney
42	chr1:161101400-161103600	Active TSS	Gastric	stomach
43	chr1:161101400-161103600	Active TSS	Ovary	ovary
44	chr1:161101400-161103800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
45	chr1:161101400-161103800	Active TSS	Right Atrium	heart
46	chr1:161101400-161103800	Active TSS	NHDF-Ad	bronchial
47	chr1:161101400-161103800	Active TSS	Osteobl	bone
48	chr1:161101400-161104000	Active TSS	iPS-18 Cell Line	embryonic stem cell
49	chr1:161101400-161104000	Active TSS	A549	lung
50	chr1:161101600-161103200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--

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