Variant report

Variant	rs238528
Chromosome Location	chr12:58132748-58132749
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	MAZ	chr12:58132667-58133058	K562	blood:	n/a	chr12:58132910-58132920
2	RFX5	chr12:58132693-58133033	H1-hESC	embryonic stem cell:	n/a	n/a
3	ZBTB7A	chr12:58132384-58132993	K562	blood:	n/a	n/a
4	ATF2	chr12:58132662-58133069	H1-hESC	embryonic stem cell:	n/a	n/a
5	SIN3AK20	chr12:58132670-58133050	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr12:58132258-58133084	H1-neurons	neurons:	n/a	n/a
7	EP300	chr12:58132646-58132989	SK-N-SH_RA	brain:	n/a	n/a
8	ZBTB7A	chr12:58132628-58133032	K562	blood:	n/a	n/a
9	JUND	chr12:58132694-58133016	H1-hESC	embryonic stem cell:	n/a	n/a
10	ZBTB7A	chr12:58132436-58133121	ECC-1	luminal epithelium:	n/a	chr12:58133067-58133075
11	REST	chr12:58132743-58132991	SK-N-SH	brain:	n/a	n/a
12	MAZ	chr12:58132741-58133038	HepG2	liver:	n/a	chr12:58132910-58132920
13	CHD2	chr12:58132699-58133135	H1-hESC	embryonic stem cell:	n/a	n/a
14	SP1	chr12:58132559-58133063	H1-hESC	embryonic stem cell:	n/a	chr12:58132651-58132660 chr12:58132650-58132662 chr12:58132650-58132662 chr12:58132652-58132661
15	CHD1	chr12:58132621-58133184	IMR90	lung:	n/a	n/a
16	REST	chr12:58132249-58133249	H1-neurons	neurons:	n/a	chr12:58132526-58132539 chr12:58132267-58132281
17	JUND	chr12:58132669-58133175	SK-N-SH	brain:	n/a	n/a
18	EP300	chr12:58132667-58132964	SK-N-SH_RA	brain:	n/a	n/a
19	YY1	chr12:58132732-58132951	K562	blood:	n/a	n/a
20	POLR2A	chr12:58132249-58132990	H1-neurons	neurons:	n/a	n/a
21	JUND	chr12:58132609-58133168	SK-N-SH	brain:	n/a	n/a
22	TEAD4	chr12:58132660-58133049	H1-hESC	embryonic stem cell:	n/a	n/a
23	JUND	chr12:58132597-58133048	MCF-7	breast:	n/a	n/a
24	JUND	chr12:58132613-58133097	A549	lung:	n/a	n/a
25	JUND	chr12:58132717-58133155	A549	lung:	n/a	n/a
26	MAZ	chr12:58132546-58133038	IMR90	lung:	n/a	chr12:58132587-58132597 chr12:58132910-58132920
27	RFX5	chr12:58132334-58133513	SK-N-SH	brain:	n/a	chr12:58133399-58133413 chr12:58133395-58133412 chr12:58133396-58133411 chr12:58133401-58133410 chr12:58133396-58133411 chr12:58133396-58133411
28	CREB1	chr12:58132744-58132924	A549	lung:	n/a	n/a
29	SP1	chr12:58132595-58133099	K562	blood:	n/a	chr12:58133082-58133095 chr12:58132651-58132660 chr12:58132650-58132662 chr12:58132650-58132662 chr12:58132652-58132661
30	YY1	chr12:58132621-58133043	SK-N-SH_RA	brain:	n/a	n/a
31	CREB1	chr12:58132635-58133007	A549	lung:	n/a	n/a
32	SP1	chr12:58132532-58133224	A549	lung:	n/a	chr12:58133082-58133095 chr12:58132651-58132660 chr12:58132650-58132662 chr12:58132650-58132662 chr12:58132652-58132661
33	SP4	chr12:58132640-58133053	H1-hESC	embryonic stem cell:	n/a	n/a
34	JUND	chr12:58132678-58133062	H1-hESC	embryonic stem cell:	n/a	n/a
35	SIN3A	chr12:58132717-58133066	H1-hESC	embryonic stem cell:	n/a	n/a
36	MAX	chr12:58132666-58133044	SK-N-SH	brain:	n/a	chr12:58132910-58132920
37	YY1	chr12:58132739-58132978	SK-N-SH	brain:	n/a	n/a
38	YY1	chr12:58132666-58132968	SK-N-SH_RA	brain:	n/a	n/a
39	YY1	chr12:58132686-58132965	ECC-1	luminal epithelium:	n/a	n/a
40	CTCF	chr12:58132740-58132890	SK-N-SH_RA	brain:	n/a	n/a
41	SP1	chr12:58132494-58133273	A549	lung:	n/a	chr12:58133082-58133095 chr12:58132651-58132660 chr12:58132650-58132662 chr12:58132650-58132662 chr12:58132652-58132661
42	TCF12	chr12:58132550-58133185	A549	lung:	n/a	n/a
43	SP1	chr12:58132721-58133094	H1-hESC	embryonic stem cell:	n/a	n/a
44	JUN	chr12:58132720-58133052	H1-hESC	embryonic stem cell:	n/a	n/a
45	JUND	chr12:58132726-58133001	H1-hESC	embryonic stem cell:	n/a	n/a
46	TAF1	chr12:58132693-58132980	SK-N-SH	brain:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:58132733-58132783	PFSK-1	brain:	n/a
2	chr12:58132733-58132783	HIPEpiC	eye:	n/a
3	chr12:58132733-58132783	HCF	heart:	n/a
4	chr12:58132733-58132783	ECC-1	luminal epithelium:	n/a
5	chr12:58132733-58132783	LNCaP	prostate:	n/a
6	chr12:58132733-58132783	Jurkat	blood:	n/a
7	chr12:58132733-58132783	ovcar-3	ovarian:	n/a
8	chr12:58132733-58132783	NHDF-neo	bronchial:	n/a
9	chr12:58132733-58132783	HUVEC	blood vessel:	n/a
10	chr12:58132733-58132783	SK-N-SH	brain:	n/a
11	chr12:58132733-58132783	HEEpiC	esophagus:	n/a
12	chr12:58132733-58132783	RPTEC	kidney:	n/a
13	chr12:58132733-58132783	HCPEpiC	choroid plexus:	n/a
14	chr12:58132733-58132783	PANC-1	pancreas:	n/a
15	chr12:58132733-58132783	U87	brain:	n/a
16	chr12:58132733-58132783	SK-N-SH_RA	brain:	n/a
17	chr12:58132733-58132783	HL-60	blood:	n/a
18	chr12:58132733-58132783	AoSMC	blood vessel:	n/a
19	chr12:58132733-58132783	ProgFib	skin:	n/a
20	chr12:58132733-58132783	HEK293	kidney:	embryo
21	chr12:58132733-58132783	AG09319	gingival:	n/a
22	chr12:58132733-58132783	GM12892	blood:	n/a
23	chr12:58132733-58132783	GM12878	blood:	n/a
24	chr12:58132733-58132783	AG04449	skin:	fetal
25	chr12:58132733-58132783	SAEC	small airway:	n/a
26	chr12:58132733-58132783	HCT-116	colon:	n/a
27	chr12:58132733-58132783	SK-N-MC	brain:	n/a
28	chr12:58132733-58132783	HMEC	breast:	n/a
29	chr12:58132733-58132783	HRE	kidney:	n/a
30	chr12:58132733-58132783	IMR90	lung:	fetal
31	chr12:58132733-58132783	CMK	blood:	n/a
32	chr12:58132733-58132783	AG09309	skin:	n/a
33	chr12:58132733-58132783	NH-A	brain:	n/a
34	chr12:58132733-58132783	PrEC	prostate:	n/a
35	chr12:58132733-58132783	BJ	skin:	n/a
36	chr12:58132733-58132783	HNPCEpiC	eye:	n/a
37	chr12:58132733-58132783	Caco-2	colon:	n/a
38	chr12:58132733-58132783	NT2-D1	testis:	n/a
39	chr12:58132733-58132783	A549	lung:	n/a
40	chr12:58132733-58132783	GM06990	blood:	n/a
41	chr12:58132733-58132783	HPAEpiC	pulmonary alveolar:	n/a
42	chr12:58132733-58132783	HRCEpiC	kidney:	n/a
43	chr12:58132733-58132783	NB4	blood:	n/a
44	chr12:58132733-58132783	HepG2	liver:	n/a
45	chr12:58132733-58132783	SKMC	muscle:	n/a
46	chr12:58132733-58132783	AG10803	skin:	n/a
47	chr12:58132733-58132783	GM19239	blood:	n/a
48	chr12:58132733-58132783	HAEpiC	amniotic membrane:	n/a
49	chr12:58132733-58132783	HRPEpiC	eye:	n/a
50	chr12:58132733-58132783	NHBE	bronchial:	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:58119523..58120051-chr12:58132094..58132767,2	MCF-7	breast:
2	chr12:57914271..57916098-chr12:58131440..58134732,4	K562	blood:
3	chr12:57913785..57915861-chr12:58131130..58132834,2	MCF-7	breast:
4	chr12:57916381..57918711-chr12:58131475..58134282,2	MCF-7	breast:
5	chr12:57909973..57915898-chr12:58127755..58134567,15	K562	blood:

Variant related genes	Relation type
AGAP2	TF binding region
TSPAN31	TF binding region
TSPAN31	CpG island
AGAP2	CpG island
ENSG00000208028	Chromatin interaction
ENSG00000166987	Chromatin interaction
ENSG00000175197	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038741	chr12:57877355-58174506	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
2	nsv541503	chr12:57877355-58174506	Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
3	nsv899121	chr12:58079825-58177292	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	nsv559045	chr12:58112189-58165085	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
5	nsv470296	chr12:58112189-58177292	Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
6	nsv899122	chr12:58118248-58137563	Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv899123	chr12:58118248-58155023	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
8	nsv826384	chr12:58124758-58157850	Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
9	esv3363572	chr12:58129335-58133633	Strong transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
10	nsv826385	chr12:58129908-58133427	Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
11	nsv510601	chr12:58130298-58191925	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
12	esv3408774	chr12:58130710-58133658	Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
13	esv3429081	chr12:58131185-58133683	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58119600-58132800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr12:58119600-58133000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr12:58121400-58132800	Strong transcription	Thymus	Thymus
4	chr12:58127800-58133600	Weak transcription	GM12878-XiMat	blood
5	chr12:58129000-58132800	Weak transcription	Dnd41	blood
6	chr12:58129400-58133000	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr12:58129600-58132800	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
8	chr12:58129600-58133200	Enhancers	Pancreas	Pancrea
9	chr12:58129800-58133000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
10	chr12:58130200-58134200	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr12:58130600-58132800	Active TSS	Brain Anterior Caudate	brain
12	chr12:58130600-58133000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
13	chr12:58130600-58133200	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
14	chr12:58130800-58132800	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr12:58130800-58133000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
16	chr12:58130800-58133000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
17	chr12:58130800-58133000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
18	chr12:58130800-58133200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
19	chr12:58131000-58132800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr12:58131200-58132800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr12:58131200-58132800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr12:58131200-58132800	Bivalent/Poised TSS	HepG2	liver
23	chr12:58131200-58133000	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr12:58131200-58133000	Bivalent/Poised TSS	Fetal Brain Female	brain
25	chr12:58131200-58133600	Active TSS	Brain Angular Gyrus	brain
26	chr12:58131200-58134400	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr12:58131200-58138000	Weak transcription	K562	blood
28	chr12:58131400-58132800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr12:58131400-58132800	Weak transcription	Primary B cells from peripheral blood	blood
30	chr12:58131400-58132800	Bivalent/Poised TSS	A549	lung
31	chr12:58131400-58133000	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr12:58131400-58133200	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
33	chr12:58131600-58132800	Active TSS	Brain Cingulate Gyrus	brain
34	chr12:58131600-58133200	Active TSS	Right Atrium	heart
35	chr12:58131600-58133600	Bivalent/Poised TSS	Left Ventricle	heart
36	chr12:58131600-58134600	Enhancers	Primary hematopoietic stem cells	blood
37	chr12:58131800-58132800	Bivalent/Poised TSS	Breast Myoepithelial Primary Cells	Breast
38	chr12:58131800-58132800	Active TSS	Aorta	Aorta
39	chr12:58131800-58132800	Bivalent/Poised TSS	Brain Germinal Matrix	brain
40	chr12:58131800-58133000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
41	chr12:58131800-58133000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr12:58131800-58133200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr12:58131800-58138000	Weak transcription	Lung	lung
44	chr12:58132000-58132800	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr12:58132000-58132800	Bivalent/Poised TSS	Psoas Muscle	Psoas
46	chr12:58132000-58133000	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
47	chr12:58132000-58133000	Active TSS	Ovary	ovary
48	chr12:58132000-58133000	Active TSS	Right Ventricle	heart
49	chr12:58132000-58133000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
50	chr12:58132000-58134800	Weak transcription	Spleen	Spleen

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