Variant report

Variant	rs34474417
Chromosome Location	chr12:57560943-57560944
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	SP1	chr12:57560744-57561270	A549	lung:	n/a	chr12:57560867-57560876 chr12:57560862-57560876 chr12:57560865-57560877 chr12:57560866-57560876 chr12:57560865-57560877 chr12:57560830-57560844 chr12:57560866-57560875
2	CTCF	chr12:57560880-57561030	HBMEC	blood vessel:	n/a	n/a
3	STAT3	chr12:57560832-57561260	MCF10A-Er-Src	breast:	n/a	n/a
4	STAT3	chr12:57560907-57561258	MCF10A-Er-Src	breast:	n/a	n/a
5	FOS	chr12:57560784-57561252	MCF10A-Er-Src	breast:	n/a	chr12:57561048-57561059 chr12:57561045-57561056 chr12:57561007-57561014 chr12:57561047-57561055 chr12:57561045-57561057
6	RCOR1	chr12:57560529-57561409	IMR90	lung:	n/a	n/a
7	FOSL2	chr12:57560870-57561154	A549	lung:	n/a	chr12:57561048-57561059 chr12:57561007-57561014 chr12:57561047-57561055 chr12:57561045-57561057
8	MYC	chr12:57560809-57561219	MCF10A-Er-Src	breast:	n/a	chr12:57561047-57561056
9	MXI1	chr12:57560671-57561384	IMR90	lung:	n/a	n/a
10	POLR2A	chr12:57560732-57561014	HepG2	liver:	n/a	n/a
11	FOSL2	chr12:57560634-57561331	SK-N-SH	brain:	n/a	chr12:57561048-57561059 chr12:57560701-57560710 chr12:57561007-57561014 chr12:57561047-57561055 chr12:57561045-57561057
12	MAFK	chr12:57560932-57561099	HepG2	liver:	n/a	chr12:57561045-57561054
13	MAX	chr12:57560854-57561221	A549	lung:	n/a	chr12:57561047-57561056
14	JUND	chr12:57560805-57561249	A549	lung:	n/a	chr12:57561048-57561059 chr12:57561007-57561014 chr12:57561047-57561055 chr12:57561045-57561057
15	MAFK	chr12:57560873-57561146	Hela-S3	cervix:	n/a	chr12:57561045-57561054
16	MAX	chr12:57560550-57561361	A549	lung:	n/a	chr12:57561047-57561056
17	TCF12	chr12:57560566-57561231	A549	lung:	n/a	chr12:57561127-57561137
18	MAFK	chr12:57560881-57561225	K562	blood:	n/a	chr12:57561045-57561054
19	POLR2A	chr12:57559805-57561211	HepG2	liver:	n/a	n/a
20	FOS	chr12:57560748-57561266	MCF10A-Er-Src	breast:	n/a	chr12:57561048-57561059 chr12:57561045-57561056 chr12:57561007-57561014 chr12:57561047-57561055 chr12:57561045-57561057
21	POLR2A	chr12:57560829-57561002	HepG2	liver:	n/a	n/a
22	FOS	chr12:57560853-57561232	MCF10A-Er-Src	breast:	n/a	chr12:57561048-57561059 chr12:57561045-57561056 chr12:57561007-57561014 chr12:57561047-57561055 chr12:57561045-57561057
23	MYC	chr12:57560812-57561215	MCF10A-Er-Src	breast:	n/a	chr12:57561047-57561056
24	CEBPB	chr12:57560759-57561186	IMR90	lung:	n/a	n/a
25	FOS	chr12:57560875-57561243	HUVEC	blood vessel:	n/a	chr12:57561048-57561059 chr12:57561045-57561056 chr12:57561007-57561014 chr12:57561047-57561055 chr12:57561045-57561057
26	POLR2A	chr12:57557970-57562558	U87	brain:	n/a	n/a
27	MAZ	chr12:57560916-57561176	Hela-S3	cervix:	n/a	chr12:57561047-57561056
28	SP1	chr12:57560662-57561190	A549	lung:	n/a	chr12:57560867-57560876 chr12:57560699-57560708 chr12:57560862-57560876 chr12:57560865-57560877 chr12:57560866-57560876 chr12:57560865-57560877 chr12:57560830-57560844 chr12:57560866-57560875
29	FOSL2	chr12:57560700-57561314	A549	lung:	n/a	chr12:57561048-57561059 chr12:57560701-57560710 chr12:57561007-57561014 chr12:57561047-57561055 chr12:57561045-57561057
30	MAX	chr12:57560602-57561322	A549	lung:	n/a	chr12:57561047-57561056
31	POLR2A	chr12:57560192-57561414	U87	brain:	n/a	n/a
32	STAT3	chr12:57560939-57561233	MCF10A-Er-Src	breast:	n/a	n/a
33	POLR2A	chr12:57560855-57561218	Hela-S3	cervix:	n/a	n/a
34	FOS	chr12:57560748-57561254	MCF10A-Er-Src	breast:	n/a	chr12:57561048-57561059 chr12:57561045-57561056 chr12:57561007-57561014 chr12:57561047-57561055 chr12:57561045-57561057
35	STAT3	chr12:57560845-57561254	MCF10A-Er-Src	breast:	n/a	n/a
36	POLR2A	chr12:57558312-57562558	U87	brain:	n/a	n/a
37	POLR2A	chr12:57560259-57561336	U87	brain:	n/a	n/a
38	MAFK	chr12:57560823-57561219	IMR90	lung:	n/a	chr12:57561045-57561054

No.	Distal block	Cell Line	Cell type
1	chr12:57558276..57561076-chr12:57569172..57570958,2	MCF-7	breast:
2	chr12:57520220..57523882-chr12:57558135..57563846,11	MCF-7	breast:
3	chr12:57470985..57473736-chr12:57560913..57563302,2	K562	blood:
4	chr12:57480714..57483772-chr12:57558111..57562184,3	MCF-7	breast:
5	chr12:57520113..57524524-chr12:57557752..57564598,9	MCF-7	breast:

Variant related genes	Relation type
LRP1	TF binding region
ENSG00000166888	Chromatin interaction
ENSG00000166886	Chromatin interaction
ENSG00000166881	Chromatin interaction
ENSG00000123384	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs34293059	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34423990	0.89[ASN][1000 genomes]
rs34548137	0.89[ASN][1000 genomes]
rs34713147	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34736975	1.00[ASN][1000 genomes]
rs34743301	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35425257	0.81[AFR][1000 genomes]
rs35792438	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35842116	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs36049517	0.83[AFR][1000 genomes]

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	nsv1040850	chr12:57055011-57679209	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	nsv559023	chr12:57530670-57616061	Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
3	nsv518980	chr12:57532982-57637593	Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv899112	chr12:57535266-57601388	Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
5	nsv525873	chr12:57535266-57616013	Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
6	nsv899113	chr12:57543572-57601388	Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	12 gene(s)	inside rSNPs	diseases
7	nsv899114	chr12:57556768-57587839	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
8	esv1810281	chr12:57558657-57641094	Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57531800-57576000	Strong transcription	Fetal Brain Female	brain
2	chr12:57540600-57569400	Strong transcription	Brain Germinal Matrix	brain
3	chr12:57541600-57606600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:57541800-57607400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr12:57542200-57565600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr12:57546600-57565200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr12:57547000-57565200	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr12:57547000-57575600	Strong transcription	H1 Cell Line	embryonic stem cell
9	chr12:57547000-57575600	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr12:57547000-57606400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr12:57547200-57562400	Weak transcription	Small Intestine	intestine
12	chr12:57547400-57567400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr12:57547400-57575400	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr12:57547600-57575400	Strong transcription	Cortex derived primary cultured neurospheres	brain
15	chr12:57547600-57575600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
16	chr12:57547800-57565000	Strong transcription	Rectal Mucosa Donor 29	rectum
17	chr12:57547800-57565200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
18	chr12:57547800-57565400	Strong transcription	H9 Cell Line	embryonic stem cell
19	chr12:57548400-57561600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr12:57549000-57562400	Weak transcription	GM12878-XiMat	blood
21	chr12:57549000-57575200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr12:57552600-57563800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr12:57552600-57565000	Strong transcription	Fetal Stomach	stomach
24	chr12:57552800-57562400	Weak transcription	Primary hematopoietic stem cells	blood
25	chr12:57552800-57563000	Strong transcription	Ovary	ovary
26	chr12:57552800-57564200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr12:57552800-57566800	Weak transcription	Right Atrium	heart
28	chr12:57552800-57568400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr12:57552800-57575200	Strong transcription	Duodenum Mucosa	Duodenum
30	chr12:57552800-57606800	Strong transcription	Fetal Intestine Large	intestine
31	chr12:57552800-57607000	Strong transcription	Liver	Liver
32	chr12:57553000-57562600	Strong transcription	Brain Cingulate Gyrus	brain
33	chr12:57553000-57565000	Strong transcription	Duodenum Smooth Muscle	Duodenum
34	chr12:57553200-57607400	Strong transcription	Fetal Intestine Small	intestine
35	chr12:57553600-57564600	Strong transcription	Stomach Smooth Muscle	stomach
36	chr12:57553600-57565200	Strong transcription	Brain Inferior Temporal Lobe	brain
37	chr12:57553800-57563600	Strong transcription	Fetal Muscle Leg	muscle
38	chr12:57553800-57564600	Strong transcription	Colon Smooth Muscle	Colon
39	chr12:57554200-57563200	Strong transcription	Fetal Muscle Trunk	muscle
40	chr12:57554400-57568800	Strong transcription	Brain Hippocampus Middle	brain
41	chr12:57555400-57583200	Weak transcription	Fetal Heart	heart
42	chr12:57556800-57564600	Strong transcription	Adipose Nuclei	Adipose
43	chr12:57557000-57565000	Strong transcription	Placenta	Placenta
44	chr12:57557400-57606800	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr12:57558000-57561400	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr12:57558000-57561400	Genic enhancers	HSMM	muscle
47	chr12:57558000-57561400	Genic enhancers	NHDF-Ad	bronchial
48	chr12:57558000-57562400	Strong transcription	Fetal Kidney	kidney
49	chr12:57558000-57563800	Strong transcription	Colonic Mucosa	Colon
50	chr12:57558000-57565200	Strong transcription	Fetal Lung	lung

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