Variant report

Variant	rs12699414
Chromosome Location	chr7:12726253-12726254
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	ELF1	chr7:12725966-12726620	K562	blood:	n/a	chr7:12726271-12726283
2	MAX	chr7:12725843-12727519	ECC-1	luminal epithelium:	n/a	chr7:12726222-12726232 chr7:12726219-12726238 chr7:12726224-12726233 chr7:12726571-12726580 chr7:12726222-12726235
3	USF1	chr7:12725902-12726500	A549	lung:	n/a	chr7:12726298-12726314 chr7:12726431-12726447
4	CTCF	chr7:12726217-12726638	T-47D	breast:	n/a	n/a
5	MXI1	chr7:12725862-12727649	K562	blood:	n/a	n/a
6	REST	chr7:12726003-12727706	H1-neurons	neurons:	n/a	chr7:12726503-12726516 chr7:12727261-12727274 chr7:12726496-12726506 chr7:12726922-12726935 chr7:12726506-12726519
7	E2F6	chr7:12726014-12726621	K562	blood:	n/a	chr7:12726439-12726448 chr7:12726538-12726548
8	POLR2A	chr7:12725933-12727758	Hela-S3	cervix:	n/a	n/a
9	TCF12	chr7:12725733-12727571	ECC-1	luminal epithelium:	n/a	chr7:12726232-12726242
10	IRF1	chr7:12726035-12727546	K562	blood:	n/a	chr7:12727208-12727222
11	RUNX3	chr7:12725966-12726592	GM12878	blood:	n/a	n/a
12	USF1	chr7:12725853-12726503	A549	lung:	n/a	chr7:12726298-12726314 chr7:12726431-12726447
13	ZNF143	chr7:12726072-12727480	Hela-S3	cervix:	n/a	chr7:12726573-12726591 chr7:12727096-12727114 chr7:12726538-12726548
14	JUND	chr7:12725954-12727565	K562	blood:	n/a	chr7:12727172-12727181
15	POLR2A	chr7:12725962-12727578	HL-60	blood:	n/a	n/a
16	GABPA	chr7:12726125-12726465	Hela-S3	cervix:	n/a	n/a
17	MXI1	chr7:12726011-12727596	HepG2	liver:	n/a	n/a
18	FOS	chr7:12726114-12726404	MCF10A-Er-Src	breast:	n/a	n/a
19	EP300	chr7:12726093-12727519	HepG2	liver:	n/a	chr7:12726539-12726548 chr7:12727088-12727104 chr7:12726934-12726950 chr7:12726888-12726897 chr7:12726539-12726555 chr7:12726430-12726446 chr7:12726350-12726357
20	TCF7L2	chr7:12725915-12727382	HCT-116	colon:	n/a	n/a
21	NFYB	chr7:12725830-12726361	Hela-S3	cervix:	n/a	n/a
22	MAX	chr7:12725945-12727519	SK-N-SH	brain:	n/a	chr7:12726222-12726232 chr7:12726219-12726238 chr7:12726224-12726233 chr7:12726571-12726580 chr7:12726222-12726235
23	EP300	chr7:12726089-12726512	SK-N-SH_RA	brain:	n/a	chr7:12726430-12726446 chr7:12726350-12726357
24	TAF1	chr7:12726120-12727528	ECC-1	luminal epithelium:	n/a	n/a
25	MAZ	chr7:12726020-12727470	Hela-S3	cervix:	n/a	chr7:12726219-12726238 chr7:12726224-12726233 chr7:12726571-12726580 chr7:12726222-12726235
26	RCOR1	chr7:12725996-12727694	Hela-S3	cervix:	n/a	n/a
27	SRF	chr7:12725895-12727435	MCF-7	breast:	n/a	chr7:12726938-12726948
28	HEY1	chr7:12725908-12727757	K562	blood:	n/a	chr7:12726536-12726551
29	ZMIZ1	chr7:12725914-12727607	K562	blood:	n/a	n/a
30	USF1	chr7:12725783-12726630	HCT-116	colon:	n/a	chr7:12726298-12726314 chr7:12726431-12726447
31	TEAD4	chr7:12725987-12726667	ECC-1	luminal epithelium:	n/a	n/a
32	ELF1	chr7:12726044-12726647	K562	blood:	n/a	chr7:12726271-12726283
33	SIN3AK20	chr7:12725864-12726306	A549	lung:	n/a	n/a
34	YY1	chr7:12725966-12726588	ECC-1	luminal epithelium:	n/a	n/a
35	E2F6	chr7:12725933-12727386	K562	blood:	n/a	chr7:12727136-12727148 chr7:12726439-12726448 chr7:12726538-12726548
36	ELF1	chr7:12726099-12726615	GM12878	blood:	n/a	chr7:12726271-12726283
37	POLR2A	chr7:12725879-12727605	PANC-1	pancreas:	n/a	n/a
38	CTCF	chr7:12726107-12727562	K562	blood:	n/a	n/a
39	CHD2	chr7:12725983-12727358	H1-hESC	embryonic stem cell:	n/a	n/a
40	SETDB1	chr7:12725957-12727344	K562	blood:	n/a	n/a
41	CREB1	chr7:12725924-12727416	H1-hESC	embryonic stem cell:	n/a	chr7:12726151-12726164
42	SETDB1	chr7:12725870-12726456	U2OS	brain:	n/a	n/a
43	BHLHE40	chr7:12725911-12727766	K562	blood:	n/a	chr7:12726298-12726314 chr7:12726431-12726447
44	CEBPB	chr7:12725831-12726632	A549	lung:	n/a	n/a
45	TAF1	chr7:12726139-12726684	H1-hESC	embryonic stem cell:	n/a	n/a
46	CTCF	chr7:12726225-12727266	GM12878	blood:	n/a	n/a
47	SIN3AK20	chr7:12726209-12726674	K562	blood:	n/a	n/a
48	CEBPB	chr7:12726047-12726533	K562	blood:	n/a	n/a
49	YY1	chr7:12726071-12727379	HepG2	liver:	n/a	chr7:12726613-12726624
50	SIN3AK20	chr7:12725828-12727897	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:12441879..12443410-chr7:12725306..12727318,2	K562	blood:
2	chr4:184365749..184366305-chr7:12726082..12726603,2	Hela-S3	cervix:
3	chr1:32538397..32538972-chr7:12726004..12726567,2	Hela-S3	cervix:
4	chr7:12726248..12727150-chr7:39662597..39663297,2	Hela-S3	cervix:
5	chr7:12441983..12444239-chr7:12724759..12726454,2	K562	blood:
6	chr7:12724061..12726495-chr7:12959611..12962564,2	K562	blood:

Variant related genes	Relation type
ARL4A	TF binding region
ENSG00000168564	Chromatin interaction
ENSG00000146530	Chromatin interaction
ENSG00000230879	Chromatin interaction
ENSG00000121775	Chromatin interaction
ENSG00000006451	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs13221298	0.88[AMR][1000 genomes]
rs13221458	0.88[AMR][1000 genomes]
rs13222937	0.88[AMR][1000 genomes]
rs13224178	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13224841	0.83[AMR][1000 genomes]
rs13224956	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13242483	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13244046	0.88[AMR][1000 genomes]
rs2191259	1.00[ASN][1000 genomes]
rs34250068	0.88[AMR][1000 genomes]
rs34452532	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34811312	0.88[AMR][1000 genomes]
rs35044018	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35091099	0.88[AMR][1000 genomes]
rs35268481	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35908302	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs55831963	0.88[AMR][1000 genomes]
rs56031342	0.88[AMR][1000 genomes]
rs56178138	0.88[AMR][1000 genomes]
rs66620565	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs66931243	0.88[AMR][1000 genomes]
rs71529345	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71536892	0.88[AMR][1000 genomes]
rs71536895	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73048799	0.88[AMR][1000 genomes]
rs73053419	0.88[AMR][1000 genomes]
rs73053466	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73055418	0.88[AMR][1000 genomes]
rs892714	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024554	chr7:12214722-12967418	Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv538735	chr7:12214722-12967418	Bivalent/Poised TSS Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv830907	chr7:12661239-12818250	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv932020	chr7:12676890-13239551	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
5	nsv830908	chr7:12695007-12870475	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	esv1794967	chr7:12710385-12758624	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	n/a
7	nsv868830	chr7:12712753-13517417	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:12725200-12727600	Active TSS	Brain Substantia Nigra	brain
2	chr7:12725200-12730600	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr7:12725400-12726600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
4	chr7:12725400-12727600	Active TSS	Brain Hippocampus Middle	brain
5	chr7:12725400-12727800	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr7:12725400-12728000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr7:12725400-12728000	Active TSS	NHDF-Ad	bronchial
8	chr7:12725400-12728200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr7:12725400-12728800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr7:12725400-12729000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr7:12725400-12729000	Active TSS	Duodenum Smooth Muscle	Duodenum
12	chr7:12725400-12729000	Active TSS	Left Ventricle	heart
13	chr7:12725400-12729800	Active TSS	Brain Cingulate Gyrus	brain
14	chr7:12725400-12730400	Active TSS	Brain Angular Gyrus	brain
15	chr7:12725400-12730400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
16	chr7:12725400-12730400	Active TSS	Fetal Kidney	kidney
17	chr7:12725400-12730600	Active TSS	Brain Anterior Caudate	brain
18	chr7:12725600-12730800	Active TSS	Rectal Mucosa Donor 29	rectum
19	chr7:12725800-12726400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
20	chr7:12725800-12726400	Active TSS	Fetal Brain Male	brain
21	chr7:12725800-12726400	Flanking Active TSS	NH-A	brain
22	chr7:12725800-12726600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr7:12725800-12726800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
24	chr7:12725800-12727200	Active TSS	Primary T cells from cord blood	blood
25	chr7:12725800-12727200	Active TSS	Liver	Liver
26	chr7:12725800-12727400	Active TSS	NHLF	lung
27	chr7:12725800-12727600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr7:12725800-12727800	Active TSS	Primary T killer memory cells from peripheral blood	blood
29	chr7:12725800-12728000	Active TSS	Brain Germinal Matrix	brain
30	chr7:12725800-12728000	Active TSS	Colon Smooth Muscle	Colon
31	chr7:12725800-12728800	Active TSS	Rectal Mucosa Donor 31	rectum
32	chr7:12725800-12730200	Active TSS	Fetal Stomach	stomach
33	chr7:12725800-12730400	Active TSS	Fetal Intestine Small	intestine
34	chr7:12725800-12730400	Active TSS	Right Atrium	heart
35	chr7:12725800-12730600	Active TSS	Right Ventricle	heart
36	chr7:12726000-12726400	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr7:12726000-12726400	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr7:12726000-12726400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr7:12726000-12726400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
40	chr7:12726000-12726400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
41	chr7:12726000-12726400	Flanking Active TSS	Fetal Muscle Trunk	muscle
42	chr7:12726000-12726400	Flanking Active TSS	Fetal Muscle Leg	muscle
43	chr7:12726000-12726400	Flanking Active TSS	Fetal Thymus	thymus
44	chr7:12726000-12726400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
45	chr7:12726000-12726400	Flanking Active TSS	Stomach Smooth Muscle	stomach
46	chr7:12726000-12726400	Flanking Active TSS	GM12878-XiMat	blood
47	chr7:12726000-12726400	Flanking Active TSS	HepG2	liver
48	chr7:12726000-12726600	Active TSS	Colonic Mucosa	Colon
49	chr7:12726000-12727000	Active TSS	Primary T helper cells fromperipheralblood	blood
50	chr7:12726000-12727200	Active TSS	Primary T helper memory cells from peripheral blood 1	blood

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