Variant report

Variant	rs73340401
Chromosome Location	chr12:56617735-56617736
allele	A/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	TEAD4	chr12:56617704-56618416	SK-N-SH	brain:	n/a	n/a
2	BCLAF1	chr12:56617693-56618406	GM12878	blood:	n/a	n/a
3	POLR2A	chr12:56617687-56618358	HepG2	liver:	n/a	n/a
4	STAT5A	chr12:56617702-56618248	GM12878	blood:	n/a	chr12:56618106-56618126 chr12:56618112-56618121 chr12:56618112-56618120 chr12:56618111-56618120
5	PML	chr12:56617725-56618403	K562	blood:	n/a	n/a
6	TEAD4	chr12:56617610-56618438	ECC-1	luminal epithelium:	n/a	n/a
7	TEAD4	chr12:56617710-56618347	K562	blood:	n/a	n/a
8	FOSL2	chr12:56617509-56618664	A549	lung:	n/a	chr12:56618078-56618087
9	POLR2A	chr12:56617582-56618505	PANC-1	pancreas:	n/a	n/a
10	FOXM1	chr12:56617545-56618502	ECC-1	luminal epithelium:	n/a	n/a
11	SRF	chr12:56617616-56618425	MCF-7	breast:	n/a	n/a
12	REST	chr12:56617583-56619459	A549	lung:	n/a	chr12:56618946-56618966 chr12:56618947-56618965 chr12:56618951-56618960 chr12:56618952-56618966 chr12:56617967-56617976 chr12:56618946-56618966 chr12:56618949-56618962
13	CTCF	chr12:56617599-56618678	MCF-7	breast:	n/a	chr12:56617924-56617940 chr12:56617923-56617941 chr12:56617925-56617938 chr12:56617918-56617939
14	FOXM1	chr12:56617658-56618400	GM12878	blood:	n/a	n/a
15	CTCF	chr12:56617575-56618575	K562	blood:	n/a	chr12:56617924-56617940 chr12:56617923-56617941 chr12:56617925-56617938 chr12:56617918-56617939
16	CEBPB	chr12:56617657-56618138	H1-hESC	embryonic stem cell:	n/a	chr12:56618028-56618036
17	POLR2A	chr12:56617505-56618540	U87	brain:	n/a	n/a
18	RAD21	chr12:56617732-56618330	GM12878	blood:	n/a	chr12:56617931-56617938
19	RELA	chr12:56617452-56618326	GM19099	blood:	n/a	n/a
20	POLR2A	chr12:56617628-56618370	U87	brain:	n/a	n/a
21	TAF1	chr12:56617612-56618447	A549	lung:	n/a	n/a
22	TEAD4	chr12:56617703-56618410	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr12:56617733-56618438	PANC-1	pancreas:	n/a	n/a
24	SMC3	chr12:56617723-56618380	Hela-S3	cervix:	n/a	chr12:56618044-56618054 chr12:56617925-56617939
25	REST	chr12:56617694-56619521	HL-60	blood:	n/a	chr12:56618946-56618966 chr12:56618947-56618965 chr12:56618951-56618960 chr12:56618952-56618966 chr12:56617967-56617976 chr12:56618946-56618966 chr12:56618949-56618962
26	KAP1	chr12:56617730-56618224	U2OS	brain:	n/a	n/a
27	TAF1	chr12:56617654-56618423	H1-hESC	embryonic stem cell:	n/a	n/a
28	CREB1	chr12:56617715-56618382	ECC-1	luminal epithelium:	n/a	n/a
29	POLR2A	chr12:56614874-56618402	HepG2	liver:	n/a	n/a
30	GABPA	chr12:56617675-56618404	SK-N-SH	brain:	n/a	n/a
31	TEAD4	chr12:56617379-56618366	K562	blood:	n/a	n/a
32	REST	chr12:56617325-56618689	H1-neurons	neurons:	n/a	chr12:56617967-56617976
33	POLR2A	chr12:56617511-56618520	U87	brain:	n/a	n/a
34	REST	chr12:56617632-56618468	A549	lung:	n/a	chr12:56617967-56617976
35	SP1	chr12:56617484-56618557	HCT-116	colon:	n/a	chr12:56618017-56618038 chr12:56618069-56618090
36	CTCF	chr12:56617655-56618535	HepG2	liver:	n/a	chr12:56617924-56617940 chr12:56617923-56617941 chr12:56617925-56617938 chr12:56617918-56617939
37	POLR2A	chr12:56617712-56618388	Hela-S3	cervix:	n/a	n/a
38	ATF3	chr12:56617652-56618352	A549	lung:	n/a	n/a
39	HCFC1	chr12:56617356-56618758	Hela-S3	cervix:	n/a	n/a
40	CTCF	chr12:56617693-56618583	K562	blood:	n/a	chr12:56617924-56617940 chr12:56617923-56617941 chr12:56617925-56617938 chr12:56617918-56617939
41	POLR2A	chr12:56617653-56618428	HCT-116	colon:	n/a	n/a
42	HEY1	chr12:56617714-56617948	K562	blood:	n/a	n/a
43	MAX	chr12:56617682-56618406	SK-N-SH	brain:	n/a	n/a
44	E2F6	chr12:56617631-56618514	A549	lung:	n/a	chr12:56618028-56618037 chr12:56618080-56618089
45	USF1	chr12:56617674-56618333	A549	lung:	n/a	n/a
46	GABPA	chr12:56617650-56618558	A549	lung:	n/a	n/a
47	YY1	chr12:56617717-56618341	H1-hESC	embryonic stem cell:	n/a	chr12:56618038-56618052
48	RAD21	chr12:56617722-56618393	A549	lung:	n/a	chr12:56617931-56617938
49	CTCF	chr12:56617683-56618392	H1-hESC	embryonic stem cell:	n/a	chr12:56617924-56617940 chr12:56617923-56617941 chr12:56617925-56617938 chr12:56617918-56617939
50	ZBTB7A	chr12:56617673-56618787	ECC-1	luminal epithelium:	n/a	chr12:56617914-56617922

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:56617730-56617780	AG04449	skin:	fetal
2	chr12:56617730-56617780	BE2_C	brain:	n/a
3	chr12:56617730-56617780	HEK293	kidney:	embryo
4	chr12:56617730-56617780	HUVEC	blood vessel:	n/a
5	chr12:56617730-56617780	Caco-2	colon:	n/a
6	chr12:56617730-56617780	RPTEC	kidney:	n/a
7	chr12:56617730-56617780	NHBE	bronchial:	n/a
8	chr12:56617730-56617780	AG09319	gingival:	n/a
9	chr12:56617730-56617780	BJ	skin:	n/a
10	chr12:56617730-56617780	IMR90	lung:	fetal
11	chr12:56617730-56617780	HCF	heart:	n/a
12	chr12:56617730-56617780	HL-60	blood:	n/a
13	chr12:56617730-56617780	U87	brain:	n/a
14	chr12:56617730-56617780	Hepatocyte	liver:	n/a
15	chr12:56617730-56617780	HRCEpiC	kidney:	n/a
16	chr12:56617730-56617780	HRPEpiC	eye:	n/a
17	chr12:56617730-56617780	NT2-D1	testis:	n/a
18	chr12:56617730-56617780	LNCaP	prostate:	n/a
19	chr12:56617730-56617780	HCT-116	colon:	n/a
20	chr12:56617730-56617780	HEEpiC	esophagus:	n/a
21	chr12:56617730-56617780	GM12878	blood:	n/a
22	chr12:56617730-56617780	SAEC	small airway:	n/a
23	chr12:56617730-56617780	SKMC	muscle:	n/a
24	chr12:56617730-56617780	HNPCEpiC	eye:	n/a
25	chr12:56617730-56617780	SK-N-SH_RA	brain:	n/a
26	chr12:56617730-56617780	HCM	heart:	n/a
27	chr12:56617730-56617780	NH-A	brain:	n/a
28	chr12:56617730-56617780	ECC-1	luminal epithelium:	n/a
29	chr12:56617730-56617780	T-47D	breast:	n/a
30	chr12:56617730-56617780	HCPEpiC	choroid plexus:	n/a
31	chr12:56617730-56617780	AoSMC	blood vessel:	n/a
32	chr12:56617730-56617780	HepG2	liver:	n/a
33	chr12:56617730-56617780	PrEC	prostate:	n/a
34	chr12:56617730-56617780	NHDF-neo	bronchial:	n/a
35	chr12:56617730-56617780	GM19239	blood:	n/a
36	chr12:56617730-56617780	HMEC	breast:	n/a
37	chr12:56617730-56617780	GM06990	blood:	n/a
38	chr12:56617730-56617780	Jurkat	blood:	n/a
39	chr12:56617730-56617780	HAEpiC	amniotic membrane:	n/a
40	chr12:56617730-56617780	GM12892	blood:	n/a
41	chr12:56617730-56617780	HRE	kidney:	n/a
42	chr12:56617730-56617780	HPAEpiC	pulmonary alveolar:	n/a
43	chr12:56617730-56617780	ovcar-3	ovarian:	n/a
44	chr12:56617730-56617780	MCF10A-Er-Src	breast:	n/a
45	chr12:56617730-56617780	ProgFib	skin:	n/a
46	chr12:56617730-56617780	SK-N-SH	brain:	n/a
47	chr12:56617730-56617780	GM12891	blood:	n/a
48	chr12:56617730-56617780	PFSK-1	brain:	n/a
49	chr12:56617730-56617780	CMK	blood:	n/a
50	chr12:56617730-56617780	MCF-7	breast:	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:56579404..56590957-chr12:56614094..56620955,25	MCF-7	breast:
2	chr12:56512320..56514002-chr12:56617290..56618598,8	K562	blood:
3	chr12:56614513..56617977-chr12:56679402..56681953,3	K562	blood:
4	chr12:56544703..56547101-chr12:56616435..56618053,2	K562	blood:
5	chr12:56614200..56620176-chr12:56644045..56650698,8	K562	blood:
6	chr12:56614747..56618810-chr12:56659447..56662577,5	K562	blood:
7	chr12:56616329..56619020-chr12:56658943..56660947,2	MCF-7	breast:
8	chr12:56617573..56619716-chr12:56660278..56661873,2	MCF-7	breast:
9	chr12:56509441..56516191-chr12:56612345..56620104,13	K562	blood:
10	chr12:56614920..56617825-chr12:56620846..56625139,7	MCF-7	breast:
11	chr12:56579883..56589030-chr12:56613342..56620091,21	MCF-7	breast:
12	chr12:56510450..56514790-chr12:56614310..56619055,13	K562	blood:
13	chr12:56616367..56619176-chr12:56691399..56694912,3	MCF-7	breast:
14	chr12:56615078..56617831-chr12:56708226..56710350,2	MCF-7	breast:
15	chr12:56543805..56547677-chr12:56615744..56618519,4	MCF-7	breast:
16	chr12:56616136..56618079-chr12:56659447..56662234,2	K562	blood:
17	chr12:56617633..56620172-chr12:56650859..56652641,2	K562	blood:
18	chr12:56609459..56612925-chr12:56614221..56618096,8	MCF-7	breast:
19	chr12:56613850..56618210-chr12:56691526..56695895,7	MCF-7	breast:
20	chr12:56548023..56550325-chr12:56616398..56618108,2	K562	blood:
21	chr12:56614600..56619518-chr12:56692701..56695411,5	K562	blood:
22	chr12:56519631..56523356-chr12:56615060..56618173,5	K562	blood:
23	chr12:56596803..56602914-chr12:56614556..56619492,8	MCF-7	breast:
24	chr12:56582602..56584894-chr12:56615504..56618371,3	K562	blood:
25	chr12:56508592..56516532-chr12:56613723..56619321,16	MCF-7	breast:
26	chr12:56549935..56553580-chr12:56615062..56619140,6	MCF-7	breast:
27	chr12:56615624..56617857-chr12:56693691..56696506,3	K562	blood:
28	chr12:56616662..56618372-chr12:56663281..56665483,2	MCF-7	breast:
29	chr12:56509088..56512395-chr12:56615837..56618663,6	MCF-7	breast:
30	chr12:56613899..56621490-chr12:56648204..56656770,13	K562	blood:
31	chr12:56615112..56618048-chr12:56649665..56653829,3	MCF-7	breast:
32	chr12:56586759..56587327-chr12:56617579..56618099,2	K562	blood:

Variant related genes	Relation type
NABP2	TF binding region
RNF41	TF binding region
RNF41	CpG island
NABP2	CpG island
ENSG00000266023	Chromatin interaction
ENSG00000257303	Chromatin interaction
ENSG00000258317	Chromatin interaction
ENSG00000257809	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000135482	Chromatin interaction
ENSG00000062485	Chromatin interaction
ENSG00000196465	Chromatin interaction
ENSG00000139613	Chromatin interaction
ENSG00000092841	Chromatin interaction
ENSG00000139540	Chromatin interaction
ENSG00000229117	Chromatin interaction
ENSG00000181852	Chromatin interaction
ENSG00000258260	Chromatin interaction
ENSG00000258345	Chromatin interaction
ENSG00000139645	Chromatin interaction
ENSG00000135469	Chromatin interaction
ENSG00000144785	Chromatin interaction
ENSG00000257727	Chromatin interaction
ENSG00000258199	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10129008	1.00[EUR][1000 genomes]
rs10876878	1.00[EUR][1000 genomes]
rs11171754	1.00[EUR][1000 genomes]
rs11171755	1.00[EUR][1000 genomes]
rs11171777	1.00[EUR][1000 genomes]
rs11548554	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11834728	1.00[EUR][1000 genomes]
rs12309480	1.00[EUR][1000 genomes]
rs12320265	1.00[EUR][1000 genomes]
rs1274502	1.00[EUR][1000 genomes]
rs1274503	1.00[EUR][1000 genomes]
rs1405859	1.00[EUR][1000 genomes]
rs2463365	1.00[EUR][1000 genomes]
rs2695783	1.00[EUR][1000 genomes]
rs28676339	1.00[EUR][1000 genomes]
rs2930788	1.00[EUR][1000 genomes]
rs2950573	1.00[EUR][1000 genomes]
rs55887836	1.00[EUR][1000 genomes]
rs58009483	1.00[EUR][1000 genomes]
rs58349500	0.97[AFR][1000 genomes]
rs59420211	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs703823	1.00[EUR][1000 genomes]
rs74092003	1.00[EUR][1000 genomes]
rs7489249	1.00[EUR][1000 genomes]
rs773658	1.00[EUR][1000 genomes]
rs773659	1.00[EUR][1000 genomes]
rs773661	1.00[EUR][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	nsv1051961	chr12:56262220-56629427	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	284 gene(s)	inside rSNPs	diseases
2	nsv1043622	chr12:56571476-56974448	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
3	nsv541500	chr12:56571476-56974448	Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 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	chr12:56614600-56619000	Active TSS	H9 Cell Line	embryonic stem cell
2	chr12:56616200-56618000	Flanking Active TSS	Dnd41	blood
3	chr12:56616400-56617800	Enhancers	Spleen	Spleen
4	chr12:56616400-56618000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr12:56616400-56618000	Weak transcription	Gastric	stomach
6	chr12:56616400-56618000	Enhancers	Small Intestine	intestine
7	chr12:56616400-56618200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr12:56616600-56617800	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr12:56616600-56618200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr12:56616600-56619000	Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr12:56616800-56618000	Enhancers	HepG2	liver
12	chr12:56616800-56618200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr12:56617000-56617800	Flanking Active TSS	Placenta	Placenta
14	chr12:56617000-56617800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
15	chr12:56617200-56617800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
16	chr12:56617200-56617800	Flanking Active TSS	Primary T cells from cord blood	blood
17	chr12:56617200-56617800	Flanking Active TSS	Duodenum Mucosa	Duodenum
18	chr12:56617200-56617800	Flanking Active TSS	Fetal Intestine Large	intestine
19	chr12:56617200-56617800	Flanking Active TSS	Rectal Smooth Muscle	rectum
20	chr12:56617200-56617800	Flanking Active TSS	Thymus	Thymus
21	chr12:56617200-56617800	Flanking Active TSS	NHLF	lung
22	chr12:56617200-56618000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
23	chr12:56617200-56618000	Flanking Active TSS	Liver	Liver
24	chr12:56617200-56618600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
25	chr12:56617200-56618800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
26	chr12:56617200-56619000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr12:56617400-56617800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr12:56617400-56617800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
29	chr12:56617400-56617800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
30	chr12:56617400-56617800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr12:56617400-56617800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr12:56617400-56617800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
33	chr12:56617400-56617800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
34	chr12:56617400-56617800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
35	chr12:56617400-56617800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr12:56617400-56617800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
37	chr12:56617400-56617800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr12:56617400-56617800	Flanking Active TSS	Brain Anterior Caudate	brain
39	chr12:56617400-56617800	Flanking Active TSS	Brain Hippocampus Middle	brain
40	chr12:56617400-56617800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
41	chr12:56617400-56617800	Flanking Active TSS	Colon Smooth Muscle	Colon
42	chr12:56617400-56617800	Flanking Active TSS	Fetal Brain Female	brain
43	chr12:56617400-56617800	Flanking Active TSS	Fetal Heart	heart
44	chr12:56617400-56617800	Flanking Active TSS	Fetal Intestine Small	intestine
45	chr12:56617400-56617800	Flanking Active TSS	Fetal Kidney	kidney
46	chr12:56617400-56617800	Flanking Active TSS	Fetal Lung	lung
47	chr12:56617400-56617800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
48	chr12:56617400-56617800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
49	chr12:56617400-56617800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
50	chr12:56617400-56617800	Flanking Active TSS	A549	lung

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