Variant report

Variant	rs12824461
Chromosome Location	chr12:9436192-9436193
allele	A/C
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	IRF4	chr12:9436154-9438008	GM12878	blood:	n/a	n/a
2	POLR2A	chr12:9436165-9436789	A549	lung:	n/a	n/a
3	TAF1	chr12:9436180-9437326	GM12892	blood:	n/a	n/a
4	TAF1	chr12:9436158-9437281	H1-hESC	embryonic stem cell:	n/a	n/a
5	MAZ	chr12:9435993-9436736	IMR90	lung:	n/a	n/a
6	BHLHE40	chr12:9436045-9436391	GM12878	blood:	n/a	n/a
7	POLR2A	chr12:9436027-9438998	GM12892	blood:	n/a	n/a
8	TAF1	chr12:9436139-9436359	ECC-1	luminal epithelium:	n/a	n/a
9	NRF1	chr12:9435832-9436429	SK-N-SH	brain:	n/a	chr12:9436242-9436251 chr12:9436240-9436249 chr12:9436239-9436250 chr12:9436240-9436254 chr12:9436237-9436251 chr12:9436240-9436251
10	SIN3A	chr12:9436168-9436813	GM12878	blood:	n/a	n/a
11	POLR2A	chr12:9436122-9437543	H1-hESC	embryonic stem cell:	n/a	n/a
12	TAF1	chr12:9436161-9437228	HepG2	liver:	n/a	n/a
13	POLR2A	chr12:9436147-9437841	GM12892	blood:	n/a	n/a
14	POLR2A	chr12:9436088-9436997	PANC-1	pancreas:	n/a	n/a
15	MYC	chr12:9436067-9437050	K562	blood:	n/a	n/a
16	MAX	chr12:9436094-9436814	GM12878	blood:	n/a	n/a
17	POLR2A	chr12:9436171-9437212	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr12:9436126-9437735	GM12892	blood:	n/a	n/a
19	POLR2A	chr12:9436171-9437355	GM12878	blood:	n/a	n/a
20	TAF1	chr12:9436117-9437287	H1-hESC	embryonic stem cell:	n/a	n/a
21	TAF1	chr12:9436171-9436786	HepG2	liver:	n/a	n/a
22	FOXA2	chr12:9436150-9436707	A549	lung:	n/a	n/a
23	GABPA	chr12:9436178-9436723	GM12878	blood:	n/a	chr12:9436242-9436251 chr12:9436240-9436249 chr12:9436240-9436254 chr12:9436237-9436251 chr12:9436240-9436251
24	TCF12	chr12:9436152-9436888	GM12878	blood:	n/a	n/a
25	SIN3AK20	chr12:9436181-9437247	HepG2	liver:	n/a	n/a
26	ARID3A	chr12:9435670-9436330	K562	blood:	n/a	n/a
27	POLR2A	chr12:9435939-9436538	K562	blood:	n/a	n/a
28	GABPA	chr12:9436183-9436654	GM12878	blood:	n/a	chr12:9436242-9436251 chr12:9436240-9436249 chr12:9436240-9436254 chr12:9436237-9436251 chr12:9436240-9436251
29	MAX	chr12:9436104-9437007	K562	blood:	n/a	n/a
30	GABPA	chr12:9435993-9436713	A549	lung:	n/a	chr12:9436242-9436251 chr12:9436240-9436249 chr12:9436240-9436254 chr12:9436237-9436251 chr12:9436240-9436251
31	IRF1	chr12:9435926-9436650	K562	blood:	n/a	chr12:9436022-9436036 chr12:9436295-9436309 chr12:9436022-9436032
32	ELF1	chr12:9436135-9436635	GM12878	blood:	n/a	chr12:9436521-9436532 chr12:9436249-9436261 chr12:9436521-9436532
33	SIN3AK20	chr12:9436182-9437147	HepG2	liver:	n/a	n/a
34	FOSL2	chr12:9436144-9437233	HepG2	liver:	n/a	n/a
35	POLR2A	chr12:9436134-9436801	HepG2	liver:	n/a	n/a
36	POLR2A	chr12:9436114-9436851	Gliobla	brain:	n/a	n/a
37	PAX5	chr12:9436045-9437271	GM12878	blood:	n/a	chr12:9436374-9436393
38	POLR2A	chr12:9436173-9436795	HUVEC	blood vessel:	n/a	n/a
39	GATA2	chr12:9435775-9436353	SH-SY5Y	brain:	n/a	chr12:9435998-9436015 chr12:9435997-9436006
40	PAX5	chr12:9436166-9437227	GM12878	blood:	n/a	chr12:9436374-9436393
41	POLR2A	chr12:9436162-9436925	Hela-S3	cervix:	n/a	n/a
42	SIN3AK20	chr12:9436189-9437024	A549	lung:	n/a	n/a
43	POLR2A	chr12:9435898-9436516	GM12878	blood:	n/a	n/a
44	POLR2A	chr12:9436184-9436399	Hela-S3	cervix:	n/a	n/a
45	IRF1	chr12:9435942-9436651	K562	blood:	n/a	chr12:9436022-9436036 chr12:9436295-9436309 chr12:9436022-9436032
46	POLR2A	chr12:9435577-9437200	MCF10A-Er-Src	breast:	n/a	n/a
47	POLR2A	chr12:9436026-9436926	PANC-1	pancreas:	n/a	n/a
48	GATA3	chr12:9435805-9436211	SH-SY5Y	brain:	n/a	chr12:9435998-9436015 chr12:9435997-9436006
49	POLR2A	chr12:9436155-9437160	H1-hESC	embryonic stem cell:	n/a	n/a
50	RUNX3	chr12:9436180-9436707	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:9428390..9430208-chr12:9433960..9436399,2	K562	blood:
2	chr12:9436030..9436711-chr12:9600583..9601103,2	HCT-116	colon:
3	chr12:9435913..9436700-chr12:31226425..31227148,3	HCT-116	colon:
4	chr12:9436173..9436735-chr12:31226434..31227168,3	Hela-S3	cervix:
5	chr12:9436150..9437103-chr12:9600374..9601086,2	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000111788	TF binding region
ENSG00000111788	Chromatin interaction
ENSG00000214826	Chromatin interaction
ENSG00000245614	Chromatin interaction
ENSG00000256069	Chromatin interaction
ENSG00000013573	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10771440	0.80[EUR][1000 genomes]
rs10771443	0.80[EUR][1000 genomes]
rs10771445	0.82[EUR][1000 genomes]
rs10843242	0.83[EUR][1000 genomes]
rs10843243	0.83[EUR][1000 genomes]
rs10843244	0.83[EUR][1000 genomes]
rs11611191	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12579328	0.86[CHB][hapmap]
rs12581534	0.92[CEU][hapmap];0.87[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12815281	0.91[CEU][hapmap];0.87[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12816390	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12822417	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs187536	0.83[EUR][1000 genomes]
rs194037	0.83[EUR][1000 genomes]
rs2059760	0.87[CEU][hapmap];0.80[EUR][1000 genomes]
rs2059761	0.80[EUR][1000 genomes]
rs252027	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs252028	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs252029	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs252030	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs252032	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs252033	0.83[EUR][1000 genomes]
rs34332	0.80[EUR][1000 genomes]
rs34333	0.80[EUR][1000 genomes]
rs34334	0.80[EUR][1000 genomes]
rs34856550	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4883225	0.87[CEU][hapmap]
rs4883226	0.84[EUR][1000 genomes]
rs55913537	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56288591	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61916195	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7299846	0.80[EUR][1000 genomes]
rs7316531	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7958291	0.80[EUR][1000 genomes]
rs7967738	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs7974378	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs7976100	0.80[EUR][1000 genomes]
rs7980256	0.88[CEU][hapmap];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045317	chr12:9113216-9544655	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
2	nsv1048491	chr12:9208806-9544655	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
3	nsv523958	chr12:9303440-9549072	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
4	nsv557355	chr12:9309995-9529015	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
5	nsv1035953	chr12:9314481-9544655	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
6	nsv427903	chr12:9371593-9830668	Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
7	esv2758293	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
8	esv2759878	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
9	nsv916832	chr12:9397450-9693952	ZNF genes & repeats Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
10	nsv976736	chr12:9431362-9524845	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs12824461	A2MP1	cis	Adipose Subcutaneous	GTEx
rs12824461	RP11-22B23.1	cis	Nerve Tibial	GTEx
rs12824461	RP11-22B23.1	cis	Artery Tibial	GTEx
rs12824461	RP11-22B23.1	cis	Skin Sun Exposed Lower leg	GTEx
rs12824461	RP11-22B23.1	cis	lung	GTEx
rs12824461	DDX12P	cis	Nerve Tibial	GTEx
rs12824461	RP11-22B23.1	cis	Whole Blood	GTEx
rs12824461	DDX12P	cis	Thyroid	GTEx
rs12824461	DDX12P	cis	Artery Tibial	GTEx
rs12824461	DDX12P	cis	Muscle Skeletal	GTEx
rs12824461	RP11-22B23.1	cis	Thyroid	GTEx
rs12824461	A2MP1	cis	Nerve Tibial	GTEx
rs12824461	RP11-22B23.1	cis	Muscle Skeletal	GTEx

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9435200-9436400	Active TSS	Fetal Brain Male	brain
2	chr12:9435400-9436200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr12:9435400-9436200	Enhancers	Fetal Heart	heart
4	chr12:9435400-9436400	Enhancers	Hela-S3	cervix
5	chr12:9435400-9437800	Active TSS	A549	lung
6	chr12:9435400-9464000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr12:9435600-9436200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
8	chr12:9435600-9436400	Active TSS	Primary T cells from cord blood	blood
9	chr12:9435600-9437800	Active TSS	Primary hematopoietic stem cells short term culture	blood
10	chr12:9435600-9437800	Active TSS	GM12878-XiMat	blood
11	chr12:9435800-9436200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr12:9435800-9436200	Flanking Active TSS	Liver	Liver
13	chr12:9435800-9436200	Active TSS	Fetal Lung	lung
14	chr12:9435800-9436200	Flanking Active TSS	Dnd41	blood
15	chr12:9435800-9436400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr12:9435800-9436400	Active TSS	Monocytes-CD14+_RO01746	blood
17	chr12:9435800-9436600	Active TSS	Primary T killer memory cells from peripheral blood	blood
18	chr12:9435800-9437000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr12:9435800-9437000	Active TSS	Primary T helper cells fromperipheralblood	blood
20	chr12:9435800-9437000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
21	chr12:9435800-9437000	Active TSS	Brain Anterior Caudate	brain
22	chr12:9435800-9437000	Active TSS	Brain Inferior Temporal Lobe	brain
23	chr12:9435800-9437000	Active TSS	Stomach Smooth Muscle	stomach
24	chr12:9435800-9437200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr12:9435800-9437200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr12:9435800-9437200	Active TSS	Brain Substantia Nigra	brain
27	chr12:9435800-9437200	Active TSS	Duodenum Smooth Muscle	Duodenum
28	chr12:9435800-9437200	Active TSS	NHDF-Ad	bronchial
29	chr12:9435800-9437400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
30	chr12:9435800-9437400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr12:9435800-9437400	Active TSS	Fetal Brain Female	brain
32	chr12:9435800-9437600	Active TSS	HUES48 Cell Line	embryonic stem cell
33	chr12:9435800-9437600	Active TSS	Rectal Mucosa Donor 29	rectum
34	chr12:9435800-9437800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr12:9435800-9437800	Active TSS	iPS-15b Cell Line	embryonic stem cell
36	chr12:9435800-9437800	Active TSS	iPS-20b Cell Line	embryonic stem cell
37	chr12:9435800-9437800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr12:9435800-9437800	Active TSS	K562	blood
39	chr12:9436000-9436200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
40	chr12:9436000-9436200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
41	chr12:9436000-9436200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr12:9436000-9436200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
43	chr12:9436000-9436200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr12:9436000-9436200	Flanking Active TSS	Duodenum Mucosa	Duodenum
45	chr12:9436000-9436200	Flanking Active TSS	Osteobl	bone
46	chr12:9436000-9436400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr12:9436000-9436400	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr12:9436000-9436400	Active TSS	Colon Smooth Muscle	Colon
49	chr12:9436000-9436400	Active TSS	Fetal Muscle Leg	muscle
50	chr12:9436000-9436400	Active TSS	Fetal Thymus	thymus

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