Variant report

Variant	rs59869626
Chromosome Location	chr1:46645811-46645812
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	CTCF	chr1:46645780-46646218	GM19239	blood:	n/a	chr1:46646100-46646113 chr1:46646097-46646115
2	RAD21	chr1:46644999-46646485	ECC-1	luminal epithelium:	n/a	chr1:46646103-46646115 chr1:46645384-46645403 chr1:46646103-46646113 chr1:46645996-46646009 chr1:46646101-46646114 chr1:46645388-46645402 chr1:46646098-46646117
3	MYC	chr1:46645175-46646283	MCF10A-Er-Src	breast:	n/a	n/a
4	SMC3	chr1:46644994-46646341	Hela-S3	cervix:	n/a	chr1:46646103-46646113 chr1:46646099-46646113 chr1:46645388-46645402 chr1:46646150-46646160
5	MYC	chr1:46645252-46646282	MCF10A-Er-Src	breast:	n/a	n/a
6	CTCF	chr1:46645760-46645910	HCFaa	heart:	n/a	n/a
7	CTCF	chr1:46644664-46646368	SK-N-SH	brain:	n/a	chr1:46645387-46645403 chr1:46645388-46645401 chr1:46646100-46646113 chr1:46645386-46645404 chr1:46645381-46645402 chr1:46646097-46646115
8	STAT3	chr1:46645494-46646161	MCF10A-Er-Src	breast:	n/a	chr1:46645974-46645985 chr1:46645976-46645984
9	RAD21	chr1:46644954-46646547	HCT-116	colon:	n/a	chr1:46646103-46646115 chr1:46645384-46645403 chr1:46646103-46646113 chr1:46645996-46646009 chr1:46646101-46646114 chr1:46645388-46645402 chr1:46646098-46646117
10	ELK1	chr1:46645319-46646150	Hela-S3	cervix:	n/a	n/a
11	CTCF	chr1:46645720-46645870	AG04449	skin:	n/a	n/a
12	RAD21	chr1:46644945-46646339	SK-N-SH	brain:	n/a	chr1:46646103-46646115 chr1:46645384-46645403 chr1:46646103-46646113 chr1:46645996-46646009 chr1:46646101-46646114 chr1:46645388-46645402 chr1:46646098-46646117
13	CTCF	chr1:46645680-46645830	GM12874	blood:	n/a	n/a
14	MAZ	chr1:46645223-46646274	Hela-S3	cervix:	n/a	n/a
15	RAD21	chr1:46645082-46646330	Hela-S3	cervix:	n/a	chr1:46646103-46646115 chr1:46645384-46645403 chr1:46646103-46646113 chr1:46645996-46646009 chr1:46646101-46646114 chr1:46645388-46645402 chr1:46646098-46646117
16	RAD21	chr1:46645772-46646350	H1-hESC	embryonic stem cell:	n/a	chr1:46646103-46646115 chr1:46646103-46646113 chr1:46645996-46646009 chr1:46646101-46646114 chr1:46646098-46646117
17	STAT3	chr1:46645808-46646145	MCF10A-Er-Src	breast:	n/a	chr1:46645974-46645985 chr1:46645976-46645984
18	RAD21	chr1:46645807-46646436	MCF-7	breast:	n/a	chr1:46646103-46646115 chr1:46646103-46646113 chr1:46645996-46646009 chr1:46646101-46646114 chr1:46646098-46646117
19	TCF12	chr1:46645718-46646564	ECC-1	luminal epithelium:	n/a	chr1:46646147-46646157 chr1:46646107-46646117
20	SMC3	chr1:46644987-46646437	SK-N-SH	brain:	n/a	chr1:46646103-46646113 chr1:46646099-46646113 chr1:46645388-46645402 chr1:46646150-46646160
21	CTCF	chr1:46645700-46645850	GM12867	blood:	n/a	n/a
22	MXI1	chr1:46645793-46646235	Hela-S3	cervix:	n/a	n/a
23	CTCF	chr1:46645680-46645830	GM12865	blood:	n/a	n/a
24	CTCF	chr1:46645700-46645850	AG09319	gingival:	n/a	n/a
25	NFIC	chr1:46645796-46646457	ECC-1	luminal epithelium:	n/a	n/a
26	CTCF	chr1:46645004-46646345	HCT-116	colon:	n/a	chr1:46645387-46645403 chr1:46645388-46645401 chr1:46646100-46646113 chr1:46645386-46645404 chr1:46645381-46645402 chr1:46646097-46646115
27	TCF7L2	chr1:46645167-46646578	Hela-S3	cervix:	n/a	n/a
28	MAX	chr1:46645645-46646385	ECC-1	luminal epithelium:	n/a	n/a
29	CTCF	chr1:46644893-46646589	HCT-116	colon:	n/a	chr1:46645387-46645403 chr1:46645388-46645401 chr1:46646487-46646495 chr1:46646100-46646113 chr1:46645386-46645404 chr1:46645381-46645402 chr1:46646097-46646115
30	RCOR1	chr1:46645810-46646236	Hela-S3	cervix:	n/a	n/a
31	CTCF	chr1:46645806-46645814	K562	blood:	n/a	n/a
32	MAX	chr1:46645714-46646305	K562	blood:	n/a	n/a
33	RAD21	chr1:46644890-46646655	HCT-116	colon:	n/a	chr1:46646103-46646115 chr1:46645384-46645403 chr1:46646103-46646113 chr1:46645996-46646009 chr1:46646101-46646114 chr1:46645388-46645402 chr1:46646098-46646117
34	STAT3	chr1:46645733-46646146	MCF10A-Er-Src	breast:	n/a	chr1:46645974-46645985 chr1:46645976-46645984
35	TCF12	chr1:46645107-46646614	ECC-1	luminal epithelium:	n/a	chr1:46646147-46646157 chr1:46646107-46646117
36	CTCF	chr1:46645700-46645850	NHDF-neo	bronchial:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:46644247..46646808-chr1:46647316..46649049,2	MCF-7	breast:
2	chr1:46639827..46642662-chr1:46645752..46647477,2	MCF-7	breast:
3	chr1:46596322..46599867-chr1:46644378..46648277,6	K562	blood:
4	chr1:46644984..46646152-chr1:46663414..46664416,4	MCF-7	breast:
5	chr1:46502754..46504889-chr1:46644727..46646775,2	MCF-7	breast:
6	chr1:46645330..46646916-chr1:46688561..46690011,13	MCF-7	breast:
7	chr1:46640707..46642746-chr1:46643622..46645846,4	K562	blood:
8	chr1:46358179..46359900-chr1:46645424..46647208,2	MCF-7	breast:
9	chr1:46592691..46601867-chr1:46642778..46650670,25	MCF-7	breast:
10	chr1:46645693..46647679-chr1:46664615..46667608,2	K562	blood:
11	chr1:46645378..46646366-chr1:46664542..46665185,2	MCF-7	breast:
12	chr1:46639014..46642746-chr1:46643175..46646686,4	K562	blood:
13	chr1:46593944..46606364-chr1:46632700..46654752,92	MCF-7	breast:
14	chr1:46645047..46645865-chr1:46688938..46689650,2	MCF-7	breast:
15	chr1:46534589..46536956-chr1:46645759..46648288,3	K562	blood:
16	chr1:46636220..46637897-chr1:46645659..46648862,3	MCF-7	breast:
17	chr1:46636993..46639249-chr1:46644481..46646542,2	MCF-7	breast:
18	chr1:46502434..46503605-chr1:46644931..46645927,6	MCF-7	breast:
19	chr1:46643862..46647366-chr1:46664036..46667027,3	K562	blood:
20	chr1:46587981..46590645-chr1:46643628..46646166,3	MCF-7	breast:
21	chr1:46500117..46505906-chr1:46642218..46647717,9	K562	blood:
22	chr1:46506118..46508735-chr1:46643577..46646194,3	K562	blood:
23	chr1:46645259..46646856-chr1:46688566..46690033,15	K562	blood:
24	chr1:46638980..46642595-chr1:46645721..46649189,9	MCF-7	breast:
25	chr1:46505537..46508242-chr1:46645160..46646732,2	MCF-7	breast:
26	chr1:46501987..46504531-chr1:46644237..46646306,43	K562	blood:
27	chr1:46645371..46647493-chr1:46686885..46689393,2	MCF-7	breast:

Variant related genes	Relation type
PIK3R3	TF binding region
ENSG00000250719	TF binding region
TSPAN1	TF binding region
ENSG00000227857	Chromatin interaction
ENSG00000117461	Chromatin interaction
ENSG00000117472	Chromatin interaction
ENSG00000085998	Chromatin interaction
ENSG00000250719	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs2234263	1.00[AMR][1000 genomes]
rs2234265	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59843477	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60794562	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
2	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
3	nsv1005189	chr1:46335186-46949309	Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
4	nsv534946	chr1:46335186-46949309	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
5	esv2761743	chr1:46339858-47026743	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
6	nsv1006747	chr1:46476089-46655484	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv534947	chr1:46476089-46655484	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
8	nsv1006530	chr1:46544842-46655484	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
9	nsv534949	chr1:46544842-46655484	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46637800-46649600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr1:46639400-46653800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr1:46639600-46652800	Weak transcription	Brain Germinal Matrix	brain
4	chr1:46640600-46648800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr1:46640800-46656400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:46641000-46648600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr1:46641200-46646600	Weak transcription	Fetal Kidney	kidney
8	chr1:46641200-46647200	Weak transcription	HSMM	muscle
9	chr1:46641200-46647400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr1:46641200-46647600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr1:46641200-46648800	Weak transcription	HSMMtube	muscle
12	chr1:46641200-46649000	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr1:46641400-46648600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr1:46642200-46646200	Weak transcription	Lung	lung
15	chr1:46642200-46646800	Weak transcription	Spleen	Spleen
16	chr1:46642200-46648400	Weak transcription	Left Ventricle	heart
17	chr1:46642400-46648800	Weak transcription	Right Atrium	heart
18	chr1:46642400-46648800	Weak transcription	Right Ventricle	heart
19	chr1:46644400-46648400	Weak transcription	Psoas Muscle	Psoas
20	chr1:46644600-46646200	Enhancers	Fetal Intestine Small	intestine
21	chr1:46644800-46646000	Enhancers	Fetal Intestine Large	intestine
22	chr1:46644800-46646400	Enhancers	Fetal Muscle Leg	muscle
23	chr1:46644800-46651400	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr1:46645000-46646000	Enhancers	Fetal Heart	heart
25	chr1:46645000-46646000	Enhancers	GM12878-XiMat	blood
26	chr1:46645000-46646200	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr1:46645000-46646200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr1:46645000-46646200	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr1:46645000-46646200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
30	chr1:46645000-46646200	Enhancers	HepG2	liver
31	chr1:46645000-46646400	Enhancers	Brain Angular Gyrus	brain
32	chr1:46645000-46646400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr1:46645000-46647600	Flanking Active TSS	Duodenum Mucosa	Duodenum
34	chr1:46645000-46648000	Flanking Active TSS	Hela-S3	cervix
35	chr1:46645000-46651400	Enhancers	Fetal Thymus	thymus
36	chr1:46645200-46646000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr1:46645200-46646000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr1:46645200-46646000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
39	chr1:46645200-46646200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr1:46645200-46646200	Enhancers	HUVEC	blood vessel
41	chr1:46645200-46646400	Enhancers	Brain Cingulate Gyrus	brain
42	chr1:46645200-46648800	Active TSS	Rectal Smooth Muscle	rectum
43	chr1:46645200-46649800	Enhancers	Placenta	Placenta
44	chr1:46645200-46650200	Enhancers	Fetal Muscle Trunk	muscle
45	chr1:46645200-46651400	Enhancers	Pancreas	Pancrea
46	chr1:46645200-46657800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr1:46645400-46646000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr1:46645400-46646000	Flanking Active TSS	Brain Hippocampus Middle	brain
49	chr1:46645400-46646000	Enhancers	Dnd41	blood
50	chr1:46645400-46646200	Enhancers	Stomach Mucosa	stomach

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