Variant report

Variant	rs12736457
Chromosome Location	chr1:113258293-113258294
allele	C/G
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	ZNF143	chr1:113257830-113258432	Hela-S3	cervix:	n/a	n/a
2	USF2	chr1:113258026-113258299	GM12878	blood:	n/a	n/a
3	STAT3	chr1:113257997-113258321	MCF10A-Er-Src	breast:	n/a	chr1:113258113-113258125
4	POLR2A	chr1:113257937-113258486	SK-N-MC	brain:	n/a	n/a
5	MXI1	chr1:113257533-113258453	HepG2	liver:	n/a	n/a
6	EGR1	chr1:113257179-113258325	K562	blood:	n/a	chr1:113258138-113258148 chr1:113257987-113257998 chr1:113257987-113258001 chr1:113257986-113258000 chr1:113257952-113257966 chr1:113258177-113258190 chr1:113257969-113257983 chr1:113257986-113257999 chr1:113257989-113257998 chr1:113257986-113257999 chr1:113257988-113257998 chr1:113257988-113257998 chr1:113257992-113257999 chr1:113257986-113257999
7	ELK1	chr1:113258019-113258504	Hela-S3	cervix:	n/a	n/a
8	MAX	chr1:113256529-113258538	K562	blood:	n/a	chr1:113257988-113257997
9	SP1	chr1:113257768-113258358	H1-hESC	embryonic stem cell:	n/a	chr1:113258137-113258149 chr1:113258117-113258126 chr1:113258137-113258149 chr1:113258139-113258148 chr1:113258182-113258191 chr1:113258117-113258126 chr1:113258181-113258193 chr1:113258138-113258147 chr1:113258116-113258128 chr1:113258117-113258127 chr1:113258118-113258127 chr1:113258178-113258192
10	MAZ	chr1:113257589-113258482	GM12878	blood:	n/a	chr1:113257988-113257997
11	POLR2A	chr1:113257875-113258456	HUVEC	blood vessel:	n/a	n/a
12	MXI1	chr1:113257729-113258367	K562	blood:	n/a	n/a
13	MAX	chr1:113257525-113258543	HepG2	liver:	n/a	chr1:113257988-113257997
14	POLR2A	chr1:113258193-113258413	MCF-7	breast:	n/a	n/a
15	SIN3A	chr1:113258085-113258450	GM12878	blood:	n/a	n/a
16	HDAC2	chr1:113257983-113258449	K562	blood:	n/a	chr1:113257988-113257997
17	SIN3AK20	chr1:113257697-113258446	K562	blood:	n/a	n/a
18	POLR2A	chr1:113257621-113258383	HCT-116	colon:	n/a	n/a
19	STAT3	chr1:113257952-113258327	MCF10A-Er-Src	breast:	n/a	chr1:113258113-113258125
20	CHD2	chr1:113258020-113258363	GM12878	blood:	n/a	n/a
21	EGR1	chr1:113257127-113258312	ECC-1	luminal epithelium:	n/a	chr1:113258138-113258148 chr1:113257987-113257998 chr1:113257987-113258001 chr1:113257986-113258000 chr1:113257952-113257966 chr1:113258177-113258190 chr1:113257969-113257983 chr1:113257986-113257999 chr1:113257989-113257998 chr1:113257986-113257999 chr1:113257988-113257998 chr1:113257988-113257998 chr1:113257992-113257999 chr1:113257986-113257999
22	TBP	chr1:113257515-113258380	K562	blood:	n/a	n/a
23	TBP	chr1:113258139-113258347	Hela-S3	cervix:	n/a	n/a
24	HA-E2F1	chr1:113257519-113258668	MCF-7	breast:	n/a	chr1:113258139-113258148
25	POLR2A	chr1:113258099-113258335	Hela-S3	cervix:	n/a	n/a
26	TEAD4	chr1:113257676-113258461	K562	blood:	n/a	n/a
27	MAX	chr1:113257372-113258330	K562	blood:	n/a	chr1:113257988-113257997
28	EGR1	chr1:113256873-113258588	HCT-116	colon:	n/a	chr1:113258138-113258148 chr1:113257987-113257998 chr1:113257987-113258001 chr1:113257986-113258000 chr1:113257952-113257966 chr1:113258177-113258190 chr1:113257969-113257983 chr1:113257986-113257999 chr1:113257989-113257998 chr1:113257986-113257999 chr1:113257988-113257998 chr1:113257988-113257998 chr1:113257992-113257999 chr1:113257986-113257999
29	POLR2A	chr1:113257625-113258427	HCT-116	colon:	n/a	n/a
30	POLR2A	chr1:113258111-113258426	ECC-1	luminal epithelium:	n/a	n/a
31	YY1	chr1:113257959-113258328	GM12878	blood:	n/a	n/a
32	ELF1	chr1:113257954-113258306	K562	blood:	n/a	chr1:113258106-113258118
33	CTCF	chr1:113258220-113258370	AG04450	lung:	n/a	n/a
34	MAX	chr1:113257667-113258340	NB4	blood:	n/a	chr1:113257988-113257997
35	CTCF	chr1:113258240-113258390	NHEK	skin:	n/a	n/a
36	MYC	chr1:113257267-113258336	K562	blood:	n/a	chr1:113257988-113257997
37	MAX	chr1:113257582-113258410	H1-hESC	embryonic stem cell:	n/a	chr1:113257988-113257997
38	EGR1	chr1:113257753-113258354	MCF-7	breast:	n/a	chr1:113258138-113258148 chr1:113257987-113257998 chr1:113257987-113258001 chr1:113257986-113258000 chr1:113257952-113257966 chr1:113258177-113258190 chr1:113257969-113257983 chr1:113257986-113257999 chr1:113257989-113257998 chr1:113257986-113257999 chr1:113257988-113257998 chr1:113257988-113257998 chr1:113257992-113257999 chr1:113257986-113257999
39	TBP	chr1:113258088-113258423	H1-hESC	embryonic stem cell:	n/a	n/a
40	MAZ	chr1:113257653-113258565	Hela-S3	cervix:	n/a	chr1:113257988-113257997
41	POLR2A	chr1:113257861-113258387	HUVEC	blood vessel:	n/a	n/a
42	REST	chr1:113257894-113259461	H1-neurons	neurons:	n/a	chr1:113259138-113259147
43	TBL1XR1	chr1:113257776-113258503	GM12878	blood:	n/a	n/a
44	SMC3	chr1:113258075-113258466	Hela-S3	cervix:	n/a	n/a
45	STAT3	chr1:113257949-113258324	MCF10A-Er-Src	breast:	n/a	chr1:113258113-113258125
46	IRF1	chr1:113257527-113258433	K562	blood:	n/a	chr1:113258114-113258128 chr1:113258135-113258149 chr1:113258181-113258195
47	POLR2A	chr1:113257693-113258427	Raji	blood:	n/a	n/a
48	POLR2A	chr1:113257645-113258432	GM18951	blood:	n/a	n/a
49	MAX	chr1:113257258-113258504	ECC-1	luminal epithelium:	n/a	chr1:113257988-113257997
50	HMGN3	chr1:113256903-113258535	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:113160555..113166228-chr1:113255932..113262161,8	K562	blood:
2	chr1:113258144..113259666-chr1:113261465..113263910,2	K562	blood:
3	chr1:113257176..113260368-chr1:113260579..113263250,3	K562	blood:
4	chr1:113257532..113261488-chr1:113614794..113617265,4	K562	blood:
5	chr1:113160602..113163896-chr1:113252357..113259247,7	K562	blood:
6	chr1:113257309..113258998-chr1:114446539..114449479,2	K562	blood:
7	chr1:113215712..113221627-chr1:113253708..113259381,5	MCF-7	breast:
8	chr1:113254236..113255978-chr1:113257610..113260572,2	MCF-7	breast:
9	chr1:113253460..113256284-chr1:113256871..113259194,3	MCF-7	breast:
10	chr1:113257500..113258462-chr12:46765998..46766576,2	HCT-116	colon:
11	chr1:113239573..113244483-chr1:113252369..113259292,10	K562	blood:
12	chr1:113160638..113164364-chr1:113256565..113260015,7	MCF-7	breast:
13	chr1:113255626..113260544-chr1:113496476..113500122,4	K562	blood:
14	chr1:113258208..113260404-chr1:113615515..113617358,3	MCF-7	breast:
15	chr1:113160649..113163501-chr1:113258154..113260079,2	MCF-7	breast:
16	chr1:113215800..113219074-chr1:113254460..113258669,6	MCF-7	breast:

Variant related genes	Relation type
PPM1J	TF binding region
ENSG00000261595	TF binding region
FAM19A3	TF binding region
ENSG00000271810	TF binding region
ENSG00000155380	Chromatin interaction
ENSG00000155363	Chromatin interaction
ENSG00000118655	Chromatin interaction
ENSG00000198799	Chromatin interaction
ENSG00000116489	Chromatin interaction
ENSG00000184599	Chromatin interaction
ENSG00000134294	Chromatin interaction
ENSG00000007341	Chromatin interaction
ENSG00000134262	Chromatin interaction
ENSG00000238198	Chromatin interaction
ENSG00000155367	Chromatin interaction
ENSG00000226419	Chromatin interaction
ENSG00000271810	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12722725	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12722910	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12724682	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12729635	1.00[ASN][1000 genomes]
rs12737053	1.00[ASN][1000 genomes]
rs34611728	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34731458	1.00[ASN][1000 genomes]
rs34961977	1.00[ASN][1000 genomes]
rs351366	1.00[ASN][1000 genomes]
rs35735679	1.00[ASN][1000 genomes]
rs35995150	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36087180	1.00[ASN][1000 genomes]
rs61818824	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61818825	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61818828	1.00[ASN][1000 genomes]
rs6688050	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71659381	1.00[ASN][1000 genomes]

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	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
2	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv1010276	chr1:113123932-113740584	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
4	nsv533295	chr1:113167645-113589588	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
5	nsv1012119	chr1:113214869-113759081	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
6	nsv535060	chr1:113214869-113759081	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
7	nsv529238	chr1:113229946-113759080	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
8	esv18511	chr1:113246318-113350775	Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
9	nsv998794	chr1:113246630-113310418	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
10	nsv872157	chr1:113247467-113265819	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
11	nsv547566	chr1:113248365-113301657	Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
12	nsv872158	chr1:113250888-113265819	Active TSS Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
13	nsv872159	chr1:113252091-113265819	Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	17 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	chr1:113256200-113258400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
2	chr1:113256200-113258600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
3	chr1:113256200-113259000	Flanking Active TSS	Adipose Nuclei	Adipose
4	chr1:113256400-113259000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
5	chr1:113256400-113259200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr1:113256600-113258800	Active TSS	Psoas Muscle	Psoas
7	chr1:113256600-113259000	Active TSS	H9 Cell Line	embryonic stem cell
8	chr1:113256600-113259000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr1:113256600-113259000	Flanking Active TSS	Primary B cells from cord blood	blood
10	chr1:113256600-113259000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
11	chr1:113256600-113259200	Flanking Active TSS	Primary hematopoietic stem cells	blood
12	chr1:113256600-113259200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr1:113256800-113258400	Active TSS	Brain Anterior Caudate	brain
14	chr1:113256800-113258400	Active TSS	NHEK	skin
15	chr1:113256800-113258600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
16	chr1:113256800-113258600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
17	chr1:113256800-113258600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
18	chr1:113256800-113258600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
19	chr1:113256800-113258600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
20	chr1:113256800-113258600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
21	chr1:113256800-113258600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr1:113256800-113258600	Active TSS	Brain Angular Gyrus	brain
23	chr1:113256800-113258600	Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr1:113256800-113258800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr1:113256800-113258800	Active TSS	Placenta Amnion	Placenta Amnion
26	chr1:113256800-113259000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr1:113256800-113259000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr1:113256800-113259000	Active TSS	Aorta	Aorta
29	chr1:113257000-113258400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr1:113257000-113258400	Active TSS	Breast Myoepithelial Primary Cells	Breast
31	chr1:113257000-113258400	Active TSS	HSMM	muscle
32	chr1:113257000-113258600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
33	chr1:113257000-113258600	Active TSS	NHDF-Ad	bronchial
34	chr1:113257000-113258800	Active TSS	A549	lung
35	chr1:113257000-113259000	Active TSS	Left Ventricle	heart
36	chr1:113257000-113259200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr1:113257200-113259000	Active TSS	Ovary	ovary
38	chr1:113257400-113258400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr1:113257400-113258400	Active TSS	Primary T helper naive cells from peripheral blood	blood
40	chr1:113257400-113258400	Bivalent/Poised TSS	Thymus	Thymus
41	chr1:113257400-113258400	Active TSS	K562	blood
42	chr1:113257400-113258400	Active TSS	NHLF	lung
43	chr1:113257400-113258600	Active TSS	Brain Substantia Nigra	brain
44	chr1:113257400-113258600	Active TSS	Colon Smooth Muscle	Colon
45	chr1:113257400-113258600	Active TSS	Fetal Kidney	kidney
46	chr1:113257400-113258600	Active TSS	Sigmoid Colon	Sigmoid Colon
47	chr1:113257400-113258600	Active TSS	HSMMtube	muscle
48	chr1:113257400-113259200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr1:113257600-113258400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:113257600-113258400	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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