Variant report

Variant	rs71652692
Chromosome Location	chr1:85725426-85725427
allele	G/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	TAF1	chr1:85725155-85725470	GM12892	blood:	n/a	n/a
2	SRF	chr1:85725002-85725791	MCF-7	breast:	n/a	chr1:85725495-85725505 chr1:85725385-85725395
3	SP1	chr1:85725120-85725563	H1-hESC	embryonic stem cell:	n/a	chr1:85725400-85725412 chr1:85725383-85725394 chr1:85725383-85725395 chr1:85725401-85725411 chr1:85725519-85725528 chr1:85725384-85725393 chr1:85725402-85725411 chr1:85725400-85725412 chr1:85725517-85725529 chr1:85725401-85725410 chr1:85725517-85725529 chr1:85725518-85725527 chr1:85725383-85725395 chr1:85725400-85725411 chr1:85725401-85725410
4	CTCF	chr1:85725400-85725550	HFF-Myc	foreskin:	n/a	chr1:85725437-85725450 chr1:85725436-85725452 chr1:85725441-85725450 chr1:85725435-85725453 chr1:85725438-85725448 chr1:85725437-85725450
5	RAD21	chr1:85724961-85725798	HCT-116	colon:	n/a	chr1:85724973-85724983 chr1:85724968-85724987 chr1:85725435-85725447 chr1:85724973-85724985 chr1:85725437-85725447 chr1:85725433-85725452
6	ELF1	chr1:85725126-85725584	K562	blood:	n/a	chr1:85725365-85725376 chr1:85725366-85725375 chr1:85725516-85725528 chr1:85725363-85725376
7	CTCF	chr1:85725299-85725771	Lung_OC	lung:	n/a	chr1:85725437-85725450 chr1:85725436-85725452 chr1:85725441-85725450 chr1:85725435-85725453 chr1:85725438-85725448 chr1:85725437-85725450
8	USF1	chr1:85725304-85725570	H1-hESC	embryonic stem cell:	n/a	n/a
9	CTCFL	chr1:85725306-85725539	K562	blood:	n/a	chr1:85725437-85725446
10	POLR2A	chr1:85724959-85725612	GM12878	blood:	n/a	n/a
11	SP2	chr1:85725216-85725459	K562	blood:	n/a	n/a
12	SP1	chr1:85725122-85725653	H1-hESC	embryonic stem cell:	n/a	chr1:85725400-85725412 chr1:85725383-85725394 chr1:85725383-85725395 chr1:85725401-85725411 chr1:85725519-85725528 chr1:85725384-85725393 chr1:85725402-85725411 chr1:85725400-85725412 chr1:85725517-85725529 chr1:85725401-85725410 chr1:85725517-85725529 chr1:85725518-85725527 chr1:85725383-85725395 chr1:85725400-85725411 chr1:85725401-85725410
13	CTCF	chr1:85725360-85725510	HRPEpiC	eye:	n/a	chr1:85725437-85725450 chr1:85725436-85725452 chr1:85725441-85725450 chr1:85725435-85725453 chr1:85725438-85725448 chr1:85725437-85725450
14	CTCF	chr1:85725280-85725529	SK-N-SH_RA	brain:	n/a	chr1:85725437-85725450 chr1:85725436-85725452 chr1:85725441-85725450 chr1:85725435-85725453 chr1:85725438-85725448 chr1:85725437-85725450
15	SRF	chr1:85725281-85725570	K562	blood:	n/a	chr1:85725495-85725505 chr1:85725385-85725395
16	CTCF	chr1:85725380-85725530	NHEK	skin:	n/a	chr1:85725437-85725450 chr1:85725436-85725452 chr1:85725441-85725450 chr1:85725435-85725453 chr1:85725438-85725448 chr1:85725437-85725450
17	CTCF	chr1:85725113-85725840	HCT-116	colon:	n/a	chr1:85725437-85725450 chr1:85725436-85725452 chr1:85725441-85725450 chr1:85725435-85725453 chr1:85725438-85725448 chr1:85725437-85725450
18	POLR2A	chr1:85725089-85725547	HepG2	liver:	n/a	n/a
19	CTCF	chr1:85725380-85725530	GM12875	blood:	n/a	chr1:85725437-85725450 chr1:85725436-85725452 chr1:85725441-85725450 chr1:85725435-85725453 chr1:85725438-85725448 chr1:85725437-85725450
20	HDAC2	chr1:85725363-85725675	MCF-7	breast:	n/a	n/a
21	YY1	chr1:85725092-85725472	GM12892	blood:	n/a	n/a
22	HCFC1	chr1:85724883-85725626	K562	blood:	n/a	n/a
23	CTCF	chr1:85725301-85725621	Fibrobl	skin:	n/a	chr1:85725437-85725450 chr1:85725436-85725452 chr1:85725441-85725450 chr1:85725435-85725453 chr1:85725438-85725448 chr1:85725437-85725450
24	ZEB1	chr1:85725184-85725579	GM12878	blood:	n/a	n/a
25	POLR2A	chr1:85725008-85725577	K562	blood:	n/a	n/a
26	ZC3H11A	chr1:85725185-85725629	K562	blood:	n/a	n/a
27	CTCF	chr1:85725266-85725604	GM19238	blood:	n/a	chr1:85725437-85725450 chr1:85725436-85725452 chr1:85725441-85725450 chr1:85725435-85725453 chr1:85725438-85725448 chr1:85725437-85725450
28	GABPA	chr1:85725070-85725575	H1-hESC	embryonic stem cell:	n/a	n/a
29	CTCF	chr1:85725380-85725530	HA-sp	spinal cord:	n/a	chr1:85725437-85725450 chr1:85725436-85725452 chr1:85725441-85725450 chr1:85725435-85725453 chr1:85725438-85725448 chr1:85725437-85725450
30	TAF1	chr1:85725008-85725600	K562	blood:	n/a	n/a
31	POLR2A	chr1:85725072-85725499	A549	lung:	n/a	n/a
32	ELF1	chr1:85725049-85725677	SK-N-SH	brain:	n/a	chr1:85725365-85725376 chr1:85725366-85725375 chr1:85725516-85725528 chr1:85725363-85725376
33	POLR2A	chr1:85725037-85725619	GM18505	blood:	n/a	n/a
34	MXI1	chr1:85725032-85725544	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chr1:85725035-85725618	Hela-S3	cervix:	n/a	n/a
36	ELF1	chr1:85725014-85725782	MCF-7	breast:	n/a	chr1:85725365-85725376 chr1:85725366-85725375 chr1:85725516-85725528 chr1:85725363-85725376
37	MAX	chr1:85725097-85725758	SK-N-SH	brain:	n/a	n/a
38	CTCF	chr1:85724850-85725979	SK-N-SH	brain:	n/a	chr1:85725437-85725450 chr1:85724970-85724983 chr1:85725436-85725452 chr1:85725441-85725450 chr1:85725435-85725453 chr1:85724959-85724967 chr1:85724967-85724985 chr1:85725438-85725448 chr1:85724970-85724979 chr1:85725437-85725450 chr1:85724864-85724873
39	CTCF	chr1:85725316-85725629	GM10248	blood:	n/a	chr1:85725437-85725450 chr1:85725436-85725452 chr1:85725441-85725450 chr1:85725435-85725453 chr1:85725438-85725448 chr1:85725437-85725450
40	REST	chr1:85724802-85725792	H1-neurons	neurons:	n/a	chr1:85724950-85724963 chr1:85724909-85724922 chr1:85724995-85725008 chr1:85725482-85725495
41	REST	chr1:85725048-85725570	SK-N-SH	brain:	n/a	chr1:85725482-85725495
42	CTCF	chr1:85725278-85725630	Spleen_OC	spleen:	n/a	chr1:85725437-85725450 chr1:85725436-85725452 chr1:85725441-85725450 chr1:85725435-85725453 chr1:85725438-85725448 chr1:85725437-85725450
43	RELA	chr1:85725101-85725635	GM19099	blood:	n/a	n/a
44	CTCF	chr1:85725380-85725530	GM12866	blood:	n/a	chr1:85725437-85725450 chr1:85725436-85725452 chr1:85725441-85725450 chr1:85725435-85725453 chr1:85725438-85725448 chr1:85725437-85725450
45	RAD21	chr1:85725019-85725822	HCT-116	colon:	n/a	chr1:85725435-85725447 chr1:85725437-85725447 chr1:85725433-85725452
46	TEAD4	chr1:85725142-85725613	K562	blood:	n/a	n/a
47	POLR2A	chr1:85724992-85725700	SK-N-SH	brain:	n/a	n/a
48	POLR2A	chr1:85724987-85725728	PFSK-1	brain:	n/a	n/a
49	POLR2A	chr1:85725090-85725542	GM12892	blood:	n/a	n/a
50	POLR2A	chr1:85724868-85725570	GM12878	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:85725395-85725445	MCF-7	breast:	n/a
2	chr1:85725395-85725445	NB4	blood:	n/a
3	chr1:85725395-85725445	SK-N-SH_RA	brain:	n/a
4	chr1:85725395-85725445	GM19239	blood:	n/a
5	chr1:85725395-85725445	BJ	skin:	n/a
6	chr1:85725395-85725445	Hepatocyte	liver:	n/a
7	chr1:85725395-85725445	HUVEC	blood vessel:	n/a
8	chr1:85725395-85725445	Jurkat	blood:	n/a
9	chr1:85725395-85725445	GM06990	blood:	n/a
10	chr1:85725395-85725445	T-47D	breast:	n/a
11	chr1:85725395-85725445	Hela-S3	cervix:	n/a
12	chr1:85725395-85725445	PrEC	prostate:	n/a
13	chr1:85725395-85725445	NH-A	brain:	n/a
14	chr1:85725395-85725445	GM12878	blood:	n/a
15	chr1:85725395-85725445	HCF	heart:	n/a
16	chr1:85725395-85725445	HRPEpiC	eye:	n/a
17	chr1:85725395-85725445	HCT-116	colon:	n/a
18	chr1:85725395-85725445	HL-60	blood:	n/a
19	chr1:85725395-85725445	U87	brain:	n/a
20	chr1:85725395-85725445	HEEpiC	esophagus:	n/a
21	chr1:85725395-85725445	HIPEpiC	eye:	n/a
22	chr1:85725395-85725445	H1-hESC	embryonic stem cell:	embryo
23	chr1:85725395-85725445	AG09319	gingival:	n/a
24	chr1:85725395-85725445	AG04450	lung:	fetal
25	chr1:85725395-85725445	HNPCEpiC	eye:	n/a
26	chr1:85725395-85725445	AG04449	skin:	fetal
27	chr1:85725395-85725445	HRE	kidney:	n/a
28	chr1:85725395-85725445	ProgFib	skin:	n/a
29	chr1:85725395-85725445	IMR90	lung:	fetal
30	chr1:85725395-85725445	AG09309	skin:	n/a
31	chr1:85725395-85725445	RPTEC	kidney:	n/a
32	chr1:85725395-85725445	HCM	heart:	n/a
33	chr1:85725395-85725445	NT2-D1	testis:	n/a
34	chr1:85725395-85725445	AoSMC	blood vessel:	n/a
35	chr1:85725395-85725445	GM12892	blood:	n/a
36	chr1:85725395-85725445	HRCEpiC	kidney:	n/a
37	chr1:85725395-85725445	HAEpiC	amniotic membrane:	n/a
38	chr1:85725395-85725445	PFSK-1	brain:	n/a
39	chr1:85725395-85725445	SK-N-SH	brain:	n/a
40	chr1:85725395-85725445	HEK293	kidney:	embryo
41	chr1:85725395-85725445	CMK	blood:	n/a
42	chr1:85725395-85725445	SKMC	muscle:	n/a
43	chr1:85725395-85725445	HCPEpiC	choroid plexus:	n/a
44	chr1:85725395-85725445	ECC-1	luminal epithelium:	n/a
45	chr1:85725395-85725445	K562	blood:	n/a
46	chr1:85725395-85725445	NHBE	bronchial:	n/a
47	chr1:85725395-85725445	NHDF-neo	bronchial:	n/a
48	chr1:85725395-85725445	ovcar-3	ovarian:	n/a
49	chr1:85725395-85725445	Caco-2	colon:	n/a
50	chr1:85725395-85725445	PANC-1	pancreas:	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:85724900..85725763-chr8:77912216..77912811,2	HCT-116	colon:
2	chr1:85725140..85725768-chr2:10588151..10588652,2	MCF-7	breast:
3	chr1:85666179..85667836-chr1:85723614..85725791,2	K562	blood:
4	chr1:85722628..85726570-chr1:85740869..85744448,4	MCF-7	breast:
5	chr1:85724038..85728124-chr1:85728267..85730109,3	K562	blood:
6	chr1:85723982..85727421-chr1:85728589..85731374,3	MCF-7	breast:
7	chr1:85723214..85729954-chr1:85738689..85743771,11	K562	blood:
8	chr1:85664620..85668785-chr1:85722586..85726821,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000223254	TF binding region
C1orf52	TF binding region
C1orf52	CpG island
ENSG00000223254	CpG island
ENSG00000097096	Chromatin interaction
ENSG00000223254	Chromatin interaction
ENSG00000164751	Chromatin interaction
ENSG00000115758	Chromatin interaction
ENSG00000223653	Chromatin interaction
ENSG00000142867	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10158486	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10493763	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10782544	0.90[ASN][1000 genomes]
rs11161562	0.94[ASN][1000 genomes]
rs12126112	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12126141	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12134420	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12136214	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12729231	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12757160	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17382844	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6698331	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv34165	chr1:85542040-85846249	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv830459	chr1:85589585-85786311	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	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	chr1:85723400-85725600	Active TSS	GM12878-XiMat	blood
2	chr1:85723400-85725800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr1:85723800-85726000	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr1:85723800-85726000	Active TSS	A549	lung
5	chr1:85724000-85725600	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr1:85724000-85725600	Active TSS	Thymus	Thymus
7	chr1:85724000-85725600	Active TSS	HSMMtube	muscle
8	chr1:85724000-85725800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr1:85724000-85725800	Active TSS	Ovary	ovary
10	chr1:85724000-85725800	Active TSS	Right Ventricle	heart
11	chr1:85724000-85726000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr1:85724000-85726000	Active TSS	Psoas Muscle	Psoas
13	chr1:85724000-85726200	Active TSS	Right Atrium	heart
14	chr1:85724200-85725600	Active TSS	H9 Cell Line	embryonic stem cell
15	chr1:85724200-85725600	Active TSS	iPS-20b Cell Line	embryonic stem cell
16	chr1:85724200-85725600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr1:85724200-85725600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
18	chr1:85724200-85725600	Active TSS	Fetal Intestine Large	intestine
19	chr1:85724200-85725600	Active TSS	Pancreas	Pancrea
20	chr1:85724200-85725800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr1:85724200-85725800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr1:85724200-85725800	Active TSS	Left Ventricle	heart
23	chr1:85724200-85725800	Active TSS	NHDF-Ad	bronchial
24	chr1:85724400-85725600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:85724400-85725600	Active TSS	HUES64 Cell Line	embryonic stem cell
26	chr1:85724400-85725600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr1:85724400-85725600	Active TSS	iPS-18 Cell Line	embryonic stem cell
28	chr1:85724400-85725600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr1:85724400-85725600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr1:85724400-85725600	Active TSS	Muscle Satellite Cultured Cells	--
31	chr1:85724400-85725600	Active TSS	Brain Angular Gyrus	brain
32	chr1:85724400-85725600	Active TSS	Brain Inferior Temporal Lobe	brain
33	chr1:85724400-85725600	Active TSS	Colonic Mucosa	Colon
34	chr1:85724400-85725600	Active TSS	Fetal Intestine Small	intestine
35	chr1:85724400-85725600	Active TSS	Pancreatic Islets	Pancreatic Islet
36	chr1:85724400-85725600	Active TSS	Placenta	Placenta
37	chr1:85724400-85725600	Active TSS	Gastric	stomach
38	chr1:85724400-85725600	Active TSS	Lung	lung
39	chr1:85724400-85725600	Active TSS	Rectal Mucosa Donor 29	rectum
40	chr1:85724400-85725600	Active TSS	Stomach Mucosa	stomach
41	chr1:85724400-85725600	Active TSS	HepG2	liver
42	chr1:85724400-85725600	Active TSS	HSMM	muscle
43	chr1:85724400-85725600	Active TSS	NHLF	lung
44	chr1:85724400-85725600	Active TSS	Osteobl	bone
45	chr1:85724400-85725800	Active TSS	Aorta	Aorta
46	chr1:85724400-85725800	Active TSS	Brain Anterior Caudate	brain
47	chr1:85724400-85725800	Active TSS	Brain Hippocampus Middle	brain
48	chr1:85724400-85725800	Active TSS	Esophagus	oesophagus
49	chr1:85724400-85726000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr1:85724400-85726000	Active TSS	Fetal Kidney	kidney

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