Variant report

Variant	rs539684752
Chromosome Location	chr12:123319708-123319709
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	MAX	chr12:123318862-123319768	MCF-7	breast:	n/a	n/a
2	REST	chr12:123318630-123320242	H1-neurons	neurons:	n/a	chr12:123319293-123319311 chr12:123319300-123319310 chr12:123319274-123319284
3	MAZ	chr12:123319549-123320521	K562	blood:	n/a	n/a
4	TAF1	chr12:123318840-123319746	H1-neurons	neurons:	n/a	n/a
5	TCF12	chr12:123318864-123319784	A549	lung:	n/a	n/a
6	CHD2	chr12:123318948-123320148	Hela-S3	cervix:	n/a	n/a
7	ZBTB7A	chr12:123319452-123320180	K562	blood:	n/a	n/a
8	MAZ	chr12:123318905-123319780	Hela-S3	cervix:	n/a	n/a
9	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
10	POLR2A	chr12:123318838-123321032	HUVEC	blood vessel:	n/a	n/a
11	MAZ	chr12:123319551-123319722	GM12878	blood:	n/a	n/a
12	SIN3AK20	chr12:123319105-123319711	SK-N-SH	brain:	n/a	n/a
13	MXI1	chr12:123318640-123321802	SK-N-SH	brain:	n/a	n/a
14	TAF1	chr12:123318756-123319915	H1-neurons	neurons:	n/a	n/a
15	EGR1	chr12:123318771-123319801	HCT-116	colon:	n/a	chr12:123318966-123318977 chr12:123319690-123319705 chr12:123318968-123318977 chr12:123318966-123318977 chr12:123318965-123318978 chr12:123318965-123318978 chr12:123318961-123318983 chr12:123318967-123318977 chr12:123318967-123318977 chr12:123318965-123318979
16	SP1	chr12:123318777-123319733	A549	lung:	n/a	chr12:123319628-123319640 chr12:123319630-123319639 chr12:123319613-123319627 chr12:123319636-123319650 chr12:123319609-123319623 chr12:123319629-123319643
17	ZBTB7A	chr12:123319392-123319931	ECC-1	luminal epithelium:	n/a	n/a
18	POLR2A	chr12:123318764-123319937	H1-neurons	neurons:	n/a	n/a
19	IRF1	chr12:123319681-123319752	K562	blood:	n/a	n/a
20	FOSL2	chr12:123318909-123319710	A549	lung:	n/a	n/a
21	MAX	chr12:123318714-123320318	A549	lung:	n/a	n/a
22	ZBTB7A	chr12:123318998-123320031	ECC-1	luminal epithelium:	n/a	n/a
23	HDAC2	chr12:123319443-123319740	H1-hESC	embryonic stem cell:	n/a	chr12:123319451-123319465
24	YY1	chr12:123319083-123319745	SK-N-SH_RA	brain:	n/a	n/a
25	POLR2A	chr12:123318783-123320223	H1-neurons	neurons:	n/a	n/a

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	chr12:123319262..123321924-chr12:123450152..123453465,3	K562	blood:
14	chr12:123318351..123322726-chr12:123344658..123350717,8	MCF-7	breast:
15	chr12:123319497..123321053-chr12:123333768..123335476,2	K562	blood:

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

Extended variants
information (count: 9 )
Associated
traits (count: 0)

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	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
9	esv3321940	chr12:123319399-123321597	Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	11 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	chr12:123318800-123319800	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr12:123318800-123319800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:123318800-123319800	Flanking Active TSS	Primary hematopoietic stem cells	blood
4	chr12:123318800-123319800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr12:123318800-123319800	Flanking Active TSS	Duodenum Mucosa	Duodenum
6	chr12:123318800-123319800	Flanking Active TSS	HMEC	breast
7	chr12:123318800-123320600	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr12:123318800-123320600	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr12:123318800-123320600	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr12:123318800-123321000	Active TSS	Brain Cingulate Gyrus	brain
11	chr12:123318800-123321200	Active TSS	H9 Cell Line	embryonic stem cell
12	chr12:123318800-123321200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr12:123318800-123321600	Active TSS	Brain Hippocampus Middle	brain
14	chr12:123318800-123321600	Active TSS	Ovary	ovary
15	chr12:123318800-123321600	Active TSS	Stomach Smooth Muscle	stomach
16	chr12:123318800-123322400	Active TSS	Brain Angular Gyrus	brain
17	chr12:123318800-123322400	Active TSS	Pancreatic Islets	Pancreatic Islet
18	chr12:123319000-123319800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
19	chr12:123319000-123319800	Flanking Active TSS	Primary B cells from cord blood	blood
20	chr12:123319000-123319800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
21	chr12:123319000-123319800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
22	chr12:123319000-123319800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
23	chr12:123319000-123319800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
24	chr12:123319000-123319800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
25	chr12:123319000-123319800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr12:123319000-123319800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
27	chr12:123319000-123319800	Active TSS	Fetal Kidney	kidney
28	chr12:123319000-123319800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
29	chr12:123319000-123319800	Flanking Active TSS	Placenta	Placenta
30	chr12:123319000-123319800	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
31	chr12:123319000-123319800	Flanking Active TSS	Psoas Muscle	Psoas
32	chr12:123319000-123319800	Flanking Active TSS	GM12878-XiMat	blood
33	chr12:123319000-123320400	Active TSS	H1 Cell Line	embryonic stem cell
34	chr12:123319000-123320600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr12:123319000-123320600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr12:123319000-123321000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr12:123319000-123321000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr12:123319000-123321400	Active TSS	Brain Anterior Caudate	brain
39	chr12:123319000-123321600	Active TSS	Breast Myoepithelial Primary Cells	Breast
40	chr12:123319000-123321600	Active TSS	Left Ventricle	heart
41	chr12:123319000-123321600	Active TSS	Right Ventricle	heart
42	chr12:123319000-123321800	Active TSS	Right Atrium	heart
43	chr12:123319000-123322000	Active TSS	Brain Inferior Temporal Lobe	brain
44	chr12:123319200-123319800	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr12:123319200-123319800	Flanking Active TSS	Primary B cells from peripheral blood	blood
46	chr12:123319200-123319800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
47	chr12:123319200-123319800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
48	chr12:123319200-123319800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
49	chr12:123319200-123319800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr12:123319200-123319800	Flanking Active TSS	Liver	Liver

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