Variant report

Variant	rs2234263
Chromosome Location	chr1:46646011-46646012
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	CTCF	chr1:46645780-46646218	GM19239	blood:	n/a	chr1:46646100-46646113 chr1:46646097-46646115
2	CTCF	chr1:46645927-46646247	T-47D	breast:	n/a	chr1:46646100-46646113 chr1:46646097-46646115
3	CTCF	chr1:46645974-46646226	Hela-S3	cervix:	n/a	chr1:46646100-46646113 chr1:46646097-46646115
4	CTCF	chr1:46645970-46646235	MCF-7	breast:	n/a	chr1:46646100-46646113 chr1:46646097-46646115
5	ZNF384	chr1:46645876-46646168	K562	blood:	n/a	n/a
6	CTCF	chr1:46645918-46646270	H1-hESC	embryonic stem cell:	n/a	chr1:46646100-46646113 chr1:46646097-46646115
7	RAD21	chr1:46645883-46646311	H1-hESC	embryonic stem cell:	n/a	chr1:46646103-46646115 chr1:46646103-46646113 chr1:46645996-46646009 chr1:46646101-46646114 chr1:46646098-46646117
8	MAZ	chr1:46645928-46646290	K562	blood:	n/a	n/a
9	CTCF	chr1:46645988-46646220	MCF-7	breast:	n/a	chr1:46646100-46646113 chr1:46646097-46646115
10	CTCF	chr1:46645920-46646289	HepG2	liver:	n/a	chr1:46646100-46646113 chr1:46646097-46646115
11	HMGN3	chr1:46645888-46646279	K562	blood:	n/a	n/a
12	ZNF143	chr1:46645972-46646148	K562	blood:	n/a	n/a
13	CTCF	chr1:46645849-46646303	K562	blood:	n/a	chr1:46646100-46646113 chr1:46646097-46646115
14	RXRA	chr1:46645876-46646277	H1-hESC	embryonic stem cell:	n/a	chr1:46646097-46646117 chr1:46646116-46646132
15	CTCF	chr1:46646000-46646150	GM12872	blood:	n/a	chr1:46646100-46646113 chr1:46646097-46646115
16	CTCF	chr1:46646000-46646150	MCF-7	breast:	n/a	chr1:46646100-46646113 chr1:46646097-46646115
17	MAX	chr1:46645829-46646254	K562	blood:	n/a	n/a
18	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
19	MYC	chr1:46645175-46646283	MCF10A-Er-Src	breast:	n/a	n/a
20	SMC3	chr1:46644994-46646341	Hela-S3	cervix:	n/a	chr1:46646103-46646113 chr1:46646099-46646113 chr1:46645388-46645402 chr1:46646150-46646160
21	RAD21	chr1:46645914-46646220	K562	blood:	n/a	chr1:46646103-46646115 chr1:46646103-46646113 chr1:46645996-46646009 chr1:46646101-46646114 chr1:46646098-46646117
22	ZKSCAN1	chr1:46645927-46646240	Hela-S3	cervix:	n/a	n/a
23	CTCF	chr1:46646000-46646150	HFF	foreskin:	n/a	chr1:46646100-46646113 chr1:46646097-46646115
24	CTCF	chr1:46645978-46646199	GM10248	blood:	n/a	chr1:46646100-46646113 chr1:46646097-46646115
25	CTCF	chr1:46646000-46646150	HepG2	liver:	n/a	chr1:46646100-46646113 chr1:46646097-46646115
26	CCNT2	chr1:46646011-46646233	K562	blood:	n/a	n/a
27	MYC	chr1:46645252-46646282	MCF10A-Er-Src	breast:	n/a	n/a
28	CTCF	chr1:46645960-46646110	GM12869	blood:	n/a	n/a
29	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
30	STAT3	chr1:46645494-46646161	MCF10A-Er-Src	breast:	n/a	chr1:46645974-46645985 chr1:46645976-46645984
31	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
32	POLR2A	chr1:46645907-46646320	HCT-116	colon:	n/a	n/a
33	ELK1	chr1:46645319-46646150	Hela-S3	cervix:	n/a	n/a
34	CTCF	chr1:46645997-46646194	HepG2	liver:	n/a	chr1:46646100-46646113 chr1:46646097-46646115
35	CTCF	chr1:46646000-46646150	GM12867	blood:	n/a	chr1:46646100-46646113 chr1:46646097-46646115
36	CHD2	chr1:46645979-46646197	Hela-S3	cervix:	n/a	n/a
37	CTCF	chr1:46645960-46646110	GM12866	blood:	n/a	n/a
38	NR3C1	chr1:46645942-46646298	ECC-1	luminal epithelium:	n/a	chr1:46646064-46646071
39	CTCF	chr1:46645903-46646297	K562	blood:	n/a	chr1:46646100-46646113 chr1:46646097-46646115
40	RAD21	chr1:46645882-46646295	HepG2	liver:	n/a	chr1:46646103-46646115 chr1:46646103-46646113 chr1:46645996-46646009 chr1:46646101-46646114 chr1:46646098-46646117
41	CTCF	chr1:46645903-46646227	A549	lung:	n/a	chr1:46646100-46646113 chr1:46646097-46646115
42	FOS	chr1:46645852-46646052	MCF10A-Er-Src	breast:	n/a	n/a
43	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
44	STAT3	chr1:46645919-46646155	MCF10A-Er-Src	breast:	n/a	chr1:46645974-46645985 chr1:46645976-46645984
45	CTCF	chr1:46645958-46646213	GM19238	blood:	n/a	chr1:46646100-46646113 chr1:46646097-46646115
46	CTCF	chr1:46645967-46646240	MCF-7	breast:	n/a	chr1:46646100-46646113 chr1:46646097-46646115
47	CTCF	chr1:46645917-46646343	MCF-7	breast:	n/a	chr1:46646100-46646113 chr1:46646097-46646115
48	CTCF	chr1:46646000-46646150	AG10803	skin:	n/a	chr1:46646100-46646113 chr1:46646097-46646115
49	CTCF	chr1:46646002-46646208	GM19240	blood:	n/a	chr1:46646100-46646113 chr1:46646097-46646115
50	RFX5	chr1:46645932-46646223	Hela-S3	cervix:	n/a	chr1:46646049-46646058

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:46645968-46646018	HEK293	kidney:	embryo
2	chr1:46645968-46646018	AoSMC	blood vessel:	n/a
3	chr1:46645968-46646018	A549	lung:	n/a
4	chr1:46645968-46646018	GM12892	blood:	n/a
5	chr1:46645968-46646018	K562	blood:	n/a
6	chr1:46645968-46646018	Caco-2	colon:	n/a
7	chr1:46645968-46646018	IMR90	lung:	fetal
8	chr1:46645968-46646018	BE2_C	brain:	n/a
9	chr1:46645968-46646018	PANC-1	pancreas:	n/a
10	chr1:46645968-46646018	MCF10A-Er-Src	breast:	n/a
11	chr1:46645968-46646018	SK-N-SH	brain:	n/a
12	chr1:46645968-46646018	PFSK-1	brain:	n/a
13	chr1:46645968-46646018	NHBE	bronchial:	n/a
14	chr1:46645968-46646018	HUVEC	blood vessel:	n/a
15	chr1:46645968-46646018	T-47D	breast:	n/a
16	chr1:46645968-46646018	HCPEpiC	choroid plexus:	n/a
17	chr1:46645968-46646018	CMK	blood:	n/a
18	chr1:46645968-46646018	PrEC	prostate:	n/a
19	chr1:46645968-46646018	HRPEpiC	eye:	n/a
20	chr1:46645968-46646018	HepG2	liver:	n/a
21	chr1:46645968-46646018	SK-N-SH_RA	brain:	n/a
22	chr1:46645968-46646018	HMEC	breast:	n/a
23	chr1:46645968-46646018	GM19239	blood:	n/a
24	chr1:46645968-46646018	NT2-D1	testis:	n/a
25	chr1:46645968-46646018	HEEpiC	esophagus:	n/a
26	chr1:46645968-46646018	SAEC	small airway:	n/a
27	chr1:46645968-46646018	HCT-116	colon:	n/a
28	chr1:46645968-46646018	HL-60	blood:	n/a
29	chr1:46645968-46646018	HAEpiC	amniotic membrane:	n/a
30	chr1:46645968-46646018	SK-N-MC	brain:	n/a
31	chr1:46645968-46646018	ProgFib	skin:	n/a
32	chr1:46645968-46646018	HIPEpiC	eye:	n/a
33	chr1:46645968-46646018	HNPCEpiC	eye:	n/a
34	chr1:46645968-46646018	Hela-S3	cervix:	n/a
35	chr1:46645968-46646018	AG04450	lung:	fetal
36	chr1:46645968-46646018	Jurkat	blood:	n/a
37	chr1:46645968-46646018	AG10803	skin:	n/a
38	chr1:46645968-46646018	NB4	blood:	n/a
39	chr1:46645968-46646018	AG09309	skin:	n/a
40	chr1:46645968-46646018	U87	brain:	n/a
41	chr1:46645968-46646018	NH-A	brain:	n/a
42	chr1:46645968-46646018	MCF-7	breast:	n/a
43	chr1:46645968-46646018	ECC-1	luminal epithelium:	n/a
44	chr1:46645968-46646018	GM12891	blood:	n/a
45	chr1:46645968-46646018	HPAEpiC	pulmonary alveolar:	n/a
46	chr1:46645968-46646018	H1-hESC	embryonic stem cell:	embryo
47	chr1:46645968-46646018	HCM	heart:	n/a
48	chr1:46645968-46646018	LNCaP	prostate:	n/a
49	chr1:46645968-46646018	GM06990	blood:	n/a
50	chr1:46645968-46646018	Hepatocyte	liver:	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	chr1:46358179..46359900-chr1:46645424..46647208,2	MCF-7	breast:
8	chr1:46592691..46601867-chr1:46642778..46650670,25	MCF-7	breast:
9	chr1:46645693..46647679-chr1:46664615..46667608,2	K562	blood:
10	chr1:46645378..46646366-chr1:46664542..46665185,2	MCF-7	breast:
11	chr1:46645952..46646536-chr1:46688903..46689405,2	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	chr1:46534589..46536956-chr1:46645759..46648288,3	K562	blood:
15	chr1:46636220..46637897-chr1:46645659..46648862,3	MCF-7	breast:
16	chr1:46636993..46639249-chr1:46644481..46646542,2	MCF-7	breast:
17	chr1:46643862..46647366-chr1:46664036..46667027,3	K562	blood:
18	chr1:46587981..46590645-chr1:46643628..46646166,3	MCF-7	breast:
19	chr1:46500117..46505906-chr1:46642218..46647717,9	K562	blood:
20	chr1:46506118..46508735-chr1:46643577..46646194,3	K562	blood:
21	chr1:46645259..46646856-chr1:46688566..46690033,15	K562	blood:
22	chr1:46638980..46642595-chr1:46645721..46649189,9	MCF-7	breast:
23	chr1:46645973..46650649-chr1:46685566..46691437,5	MCF-7	breast:
24	chr1:46505537..46508242-chr1:46645160..46646732,2	MCF-7	breast:
25	chr1:46501987..46504531-chr1:46644237..46646306,43	K562	blood:
26	chr1:46645371..46647493-chr1:46686885..46689393,2	MCF-7	breast:

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

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs59869626	1.00[AMR][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:104 , 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	chr1:46644800-46646400	Enhancers	Fetal Muscle Leg	muscle
22	chr1:46644800-46651400	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr1:46645000-46646200	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr1:46645000-46646200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr1:46645000-46646200	Enhancers	Brain Inferior Temporal Lobe	brain
26	chr1:46645000-46646200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
27	chr1:46645000-46646200	Enhancers	HepG2	liver
28	chr1:46645000-46646400	Enhancers	Brain Angular Gyrus	brain
29	chr1:46645000-46646400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr1:46645000-46647600	Flanking Active TSS	Duodenum Mucosa	Duodenum
31	chr1:46645000-46648000	Flanking Active TSS	Hela-S3	cervix
32	chr1:46645000-46651400	Enhancers	Fetal Thymus	thymus
33	chr1:46645200-46646200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr1:46645200-46646200	Enhancers	HUVEC	blood vessel
35	chr1:46645200-46646400	Enhancers	Brain Cingulate Gyrus	brain
36	chr1:46645200-46648800	Active TSS	Rectal Smooth Muscle	rectum
37	chr1:46645200-46649800	Enhancers	Placenta	Placenta
38	chr1:46645200-46650200	Enhancers	Fetal Muscle Trunk	muscle
39	chr1:46645200-46651400	Enhancers	Pancreas	Pancrea
40	chr1:46645200-46657800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr1:46645400-46646200	Enhancers	Stomach Mucosa	stomach
42	chr1:46645400-46646400	Enhancers	Liver	Liver
43	chr1:46645400-46646400	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr1:46645400-46646400	Enhancers	A549	lung
45	chr1:46645400-46646600	Weak transcription	Stomach Smooth Muscle	stomach
46	chr1:46645400-46647000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr1:46645400-46647200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr1:46645400-46647200	Weak transcription	NH-A	brain
49	chr1:46645400-46647800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr1:46645400-46647800	Flanking Active TSS	NHEK	skin

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