Variant report

Variant	rs547644678
Chromosome Location	chr12:123319200-123319201
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	POLR2A	chr12:123319069-123319233	MCF10A-Er-Src	breast:	n/a	n/a
2	CTCF	chr12:123318940-123319230	Caco-2	colon:	n/a	chr12:123319209-123319218
3	RFX5	chr12:123318830-123319469	Hela-S3	cervix:	n/a	n/a
4	SIN3AK20	chr12:123319155-123319534	PANC-1	pancreas:	n/a	n/a
5	MAX	chr12:123318862-123319768	MCF-7	breast:	n/a	n/a
6	REST	chr12:123318630-123320242	H1-neurons	neurons:	n/a	chr12:123319293-123319311 chr12:123319300-123319310 chr12:123319274-123319284
7	MXI1	chr12:123318903-123319691	Hela-S3	cervix:	n/a	n/a
8	MAFK	chr12:123318899-123319537	Hela-S3	cervix:	n/a	n/a
9	CTCF	chr12:123319060-123319210	HCPEpiC	choroid plexus:	n/a	n/a
10	CTCF	chr12:123319060-123319210	AG10803	skin:	n/a	n/a
11	TAF1	chr12:123319098-123319461	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr12:123318982-123319481	Hela-S3	cervix:	n/a	n/a
13	MAX	chr12:123318885-123319621	A549	lung:	n/a	n/a
14	CTCF	chr12:123319140-123319290	GM12872	blood:	n/a	chr12:123319209-123319218
15	TAF1	chr12:123318840-123319746	H1-neurons	neurons:	n/a	n/a
16	CTCF	chr12:123319160-123319310	HRE	kidney:	n/a	chr12:123319209-123319218
17	TAF1	chr12:123319167-123319391	Hela-S3	cervix:	n/a	n/a
18	GTF2F1	chr12:123318878-123319452	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr12:123319136-123319434	SK-N-SH	brain:	n/a	n/a
20	SIN3AK20	chr12:123319075-123319566	H1-hESC	embryonic stem cell:	n/a	n/a
21	RCOR1	chr12:123318892-123319468	Hela-S3	cervix:	n/a	n/a
22	ZKSCAN1	chr12:123318947-123319230	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr12:123319195-123319390	A549	lung:	n/a	n/a
24	CTCF	chr12:123319060-123319210	NHDF-neo	bronchial:	n/a	n/a
25	CTCF	chr12:123319120-123319270	GM12874	blood:	n/a	chr12:123319209-123319218
26	CEBPB	chr12:123318900-123319567	Hela-S3	cervix:	n/a	n/a
27	TCF12	chr12:123318864-123319784	A549	lung:	n/a	n/a
28	CTCF	chr12:123319120-123319270	GM12864	blood:	n/a	chr12:123319209-123319218
29	CHD2	chr12:123318948-123320148	Hela-S3	cervix:	n/a	n/a
30	KAP1	chr12:123318890-123319551	U2OS	brain:	n/a	n/a
31	EGR1	chr12:123318741-123319245	MCF-7	breast:	n/a	chr12:123318966-123318977 chr12:123318968-123318977 chr12:123318966-123318977 chr12:123318965-123318978 chr12:123318965-123318978 chr12:123318961-123318983 chr12:123318967-123318977 chr12:123318967-123318977 chr12:123318965-123318979
32	TCF7L2	chr12:123318905-123319443	Hela-S3	cervix:	n/a	n/a
33	TBP	chr12:123318971-123319387	H1-hESC	embryonic stem cell:	n/a	n/a
34	MAZ	chr12:123318905-123319780	Hela-S3	cervix:	n/a	n/a
35	SP1	chr12:123318810-123319758	A549	lung:	n/a	chr12:123319628-123319640 chr12:123319630-123319639 chr12:123319613-123319627 chr12:123319636-123319650 chr12:123319609-123319623 chr12:123319629-123319643
36	TBP	chr12:123318836-123319440	Hela-S3	cervix:	n/a	n/a
37	MAX	chr12:123318906-123319440	A549	lung:	n/a	n/a
38	POLR2A	chr12:123318838-123321032	HUVEC	blood vessel:	n/a	n/a
39	POLR2A	chr12:123318867-123319467	Hela-S3	cervix:	n/a	n/a
40	POLR2A	chr12:123318837-123319536	Hela-S3	cervix:	n/a	n/a
41	SIN3AK20	chr12:123319105-123319711	SK-N-SH	brain:	n/a	n/a
42	MXI1	chr12:123318640-123321802	SK-N-SH	brain:	n/a	n/a
43	JUN	chr12:123319144-123319252	K562	blood:	n/a	n/a
44	MAX	chr12:123318879-123319604	SK-N-SH	brain:	n/a	n/a
45	SP1	chr12:123318795-123319580	H1-hESC	embryonic stem cell:	n/a	n/a
46	SMC3	chr12:123318833-123319545	Hela-S3	cervix:	n/a	n/a
47	SIN3A	chr12:123318922-123319699	H1-hESC	embryonic stem cell:	n/a	chr12:123319301-123319310 chr12:123319274-123319283
48	MAX	chr12:123318881-123319587	H1-hESC	embryonic stem cell:	n/a	n/a
49	YY1	chr12:123318852-123319479	SK-N-SH_RA	brain:	n/a	n/a
50	CTCF	chr12:123319140-123319290	GM12878	blood:	n/a	chr12:123319209-123319218

No.	Distal block	Cell Line	Cell type
1	chr12:123317720..123322313-chr12:123372173..123377754,7	MCF-7	breast:
2	chr12:123317692..123320507-chr12:123463597..123466562,3	MCF-7	breast:
3	chr12:123318894..123320705-chr12:123342894..123344549,3	MCF-7	breast:
4	chr12:123257747..123262116-chr12:123318149..123321331,4	MCF-7	breast:
5	chr12:123318760..123321217-chr12:123449684..123452450,2	K562	blood:
6	chr12:123318632..123320877-chr12:123355595..123357643,2	MCF-7	breast:
7	chr12:123319192..123322007-chr12:123336993..123339222,2	MCF-7	breast:
8	chr12:123237061..123238610-chr12:123318389..123320839,2	MCF-7	breast:
9	chr12:123318837..123320791-chr12:123463752..123466824,3	MCF-7	breast:
10	chr12:123318920..123320804-chr12:123431971..123434703,2	MCF-7	breast:
11	chr12:123319135..123321319-chr3:160936978..160939441,2	MCF-7	breast:
12	chr12:123318440..123320805-chr12:123633475..123636263,2	MCF-7	breast:
13	chr12:123318351..123322726-chr12:123344658..123350717,8	MCF-7	breast:

Variant related genes	Relation type
HIP1R	TF binding region
ENSG00000090975	Chromatin interaction
ENSG00000150967	Chromatin interaction
ENSG00000130783	Chromatin interaction
ENSG00000130787	Chromatin interaction
ENSG00000256152	Chromatin interaction
ENSG00000139722	Chromatin interaction
ENSG00000139726	Chromatin interaction
ENSG00000182196	Chromatin interaction
ENSG00000169251	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899571	chr12:123215734-123363562	Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3388790	chr12:123275902-123655103	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv899572	chr12:123292503-123477311	Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv899573	chr12:123312051-123528405	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS 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 miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv517200	chr12:123312051-123654498	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
6	nsv899574	chr12:123316566-123360151	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	esv3373177	chr12:123318824-123321872	Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
8	esv3360797	chr12:123318974-123321472	Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:177 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123310400-123319200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:123313800-123319200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr12:123315600-123319200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr12:123316400-123319200	Weak transcription	Gastric	stomach
5	chr12:123318800-123319200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr12:123318800-123319200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr12:123318800-123319200	Enhancers	Primary B cells from peripheral blood	blood
8	chr12:123318800-123319200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr12:123318800-123319200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
10	chr12:123318800-123319200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr12:123318800-123319200	Enhancers	Liver	Liver
12	chr12:123318800-123319200	Flanking Active TSS	Brain Germinal Matrix	brain
13	chr12:123318800-123319200	Flanking Active TSS	Brain Substantia Nigra	brain
14	chr12:123318800-123319200	Active TSS	Duodenum Smooth Muscle	Duodenum
15	chr12:123318800-123319200	Flanking Active TSS	Fetal Brain Female	brain
16	chr12:123318800-123319200	Flanking Active TSS	Fetal Lung	lung
17	chr12:123318800-123319200	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr12:123318800-123319200	Active TSS	A549	lung
19	chr12:123318800-123319200	Enhancers	K562	blood
20	chr12:123318800-123319200	Flanking Active TSS	NHDF-Ad	bronchial
21	chr12:123318800-123319200	Flanking Active TSS	Osteobl	bone
22	chr12:123318800-123319400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
23	chr12:123318800-123319600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr12:123318800-123319600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
25	chr12:123318800-123319600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr12:123318800-123319600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr12:123318800-123319600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr12:123318800-123319600	Flanking Active TSS	Fetal Brain Male	brain
29	chr12:123318800-123319600	Flanking Active TSS	Fetal Heart	heart
30	chr12:123318800-123319600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
31	chr12:123318800-123319600	Flanking Active TSS	Hela-S3	cervix
32	chr12:123318800-123319600	Flanking Active TSS	HSMMtube	muscle
33	chr12:123318800-123319600	Flanking Active TSS	HUVEC	blood vessel
34	chr12:123318800-123319600	Flanking Active TSS	NHLF	lung
35	chr12:123318800-123319800	Active TSS	ES-I3 Cell Line	embryonic stem cell
36	chr12:123318800-123319800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr12:123318800-123319800	Flanking Active TSS	Primary hematopoietic stem cells	blood
38	chr12:123318800-123319800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr12:123318800-123319800	Flanking Active TSS	Duodenum Mucosa	Duodenum
40	chr12:123318800-123319800	Flanking Active TSS	HMEC	breast
41	chr12:123318800-123320600	Active TSS	HUES48 Cell Line	embryonic stem cell
42	chr12:123318800-123320600	Active TSS	HUES6 Cell Line	embryonic stem cell
43	chr12:123318800-123320600	Active TSS	iPS-20b Cell Line	embryonic stem cell
44	chr12:123318800-123321000	Active TSS	Brain Cingulate Gyrus	brain
45	chr12:123318800-123321200	Active TSS	H9 Cell Line	embryonic stem cell
46	chr12:123318800-123321200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr12:123318800-123321600	Active TSS	Brain Hippocampus Middle	brain
48	chr12:123318800-123321600	Active TSS	Ovary	ovary
49	chr12:123318800-123321600	Active TSS	Stomach Smooth Muscle	stomach
50	chr12:123318800-123322400	Active TSS	Brain Angular Gyrus	brain

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