Variant report

Variant	rs12822417
Chromosome Location	chr12:9436252-9436253
allele	A/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	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	BCL11A	chr12:9436252-9436488	GM12878	blood:	n/a	chr12:9436252-9436261
8	POLR2A	chr12:9436027-9438998	GM12892	blood:	n/a	n/a
9	TAF1	chr12:9436139-9436359	ECC-1	luminal epithelium:	n/a	n/a
10	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
11	SIN3A	chr12:9436168-9436813	GM12878	blood:	n/a	n/a
12	POLR2A	chr12:9436122-9437543	H1-hESC	embryonic stem cell:	n/a	n/a
13	TAF1	chr12:9436161-9437228	HepG2	liver:	n/a	n/a
14	POLR2A	chr12:9436147-9437841	GM12892	blood:	n/a	n/a
15	POLR2A	chr12:9436088-9436997	PANC-1	pancreas:	n/a	n/a
16	MYC	chr12:9436067-9437050	K562	blood:	n/a	n/a
17	MAX	chr12:9436094-9436814	GM12878	blood:	n/a	n/a
18	POLR2A	chr12:9436171-9437212	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr12:9436126-9437735	GM12892	blood:	n/a	n/a
20	POLR2A	chr12:9436171-9437355	GM12878	blood:	n/a	n/a
21	CEBPD	chr12:9436229-9436895	K562	blood:	n/a	n/a
22	TAF1	chr12:9436117-9437287	H1-hESC	embryonic stem cell:	n/a	n/a
23	TAF1	chr12:9436171-9436786	HepG2	liver:	n/a	n/a
24	FOXA2	chr12:9436150-9436707	A549	lung:	n/a	n/a
25	GABPA	chr12:9436178-9436723	GM12878	blood:	n/a	chr12:9436242-9436251 chr12:9436240-9436249 chr12:9436240-9436254 chr12:9436237-9436251 chr12:9436240-9436251
26	TCF12	chr12:9436152-9436888	GM12878	blood:	n/a	n/a
27	SIN3AK20	chr12:9436181-9437247	HepG2	liver:	n/a	n/a
28	ARID3A	chr12:9435670-9436330	K562	blood:	n/a	n/a
29	POLR2A	chr12:9435939-9436538	K562	blood:	n/a	n/a
30	GABPA	chr12:9436183-9436654	GM12878	blood:	n/a	chr12:9436242-9436251 chr12:9436240-9436249 chr12:9436240-9436254 chr12:9436237-9436251 chr12:9436240-9436251
31	MAX	chr12:9436104-9437007	K562	blood:	n/a	n/a
32	GABPA	chr12:9435993-9436713	A549	lung:	n/a	chr12:9436242-9436251 chr12:9436240-9436249 chr12:9436240-9436254 chr12:9436237-9436251 chr12:9436240-9436251
33	SIN3A	chr12:9436220-9436410	H1-hESC	embryonic stem cell:	n/a	n/a
34	IRF1	chr12:9435926-9436650	K562	blood:	n/a	chr12:9436022-9436036 chr12:9436295-9436309 chr12:9436022-9436032
35	ELF1	chr12:9436135-9436635	GM12878	blood:	n/a	chr12:9436521-9436532 chr12:9436249-9436261 chr12:9436521-9436532
36	TAF1	chr12:9436210-9436844	GM12878	blood:	n/a	n/a
37	BCL11A	chr12:9436213-9436749	GM12878	blood:	n/a	chr12:9436247-9436260 chr12:9436252-9436261 chr12:9436523-9436532
38	SIN3AK20	chr12:9436182-9437147	HepG2	liver:	n/a	n/a
39	REST	chr12:9436220-9436857	HepG2	liver:	n/a	n/a
40	FOSL2	chr12:9436144-9437233	HepG2	liver:	n/a	n/a
41	EP300	chr12:9436251-9436569	GM12878	blood:	n/a	chr12:9436524-9436531
42	POLR2A	chr12:9436134-9436801	HepG2	liver:	n/a	n/a
43	POLR2A	chr12:9436114-9436851	Gliobla	brain:	n/a	n/a
44	PAX5	chr12:9436045-9437271	GM12878	blood:	n/a	chr12:9436374-9436393
45	TBL1XR1	chr12:9436208-9436404	GM12878	blood:	n/a	n/a
46	POLR2A	chr12:9436173-9436795	HUVEC	blood vessel:	n/a	n/a
47	GATA2	chr12:9435775-9436353	SH-SY5Y	brain:	n/a	chr12:9435998-9436015 chr12:9435997-9436006
48	PAX5	chr12:9436166-9437227	GM12878	blood:	n/a	chr12:9436374-9436393
49	POLR2A	chr12:9436162-9436925	Hela-S3	cervix:	n/a	n/a
50	SIN3AK20	chr12:9436189-9437024	A549	lung:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:9436242-9436292	Caco-2	colon:	n/a
2	chr12:9436242-9436292	NH-A	brain:	n/a
3	chr12:9436248-9436298	NHBE	bronchial:	n/a
4	chr12:9436242-9436292	HRCEpiC	kidney:	n/a
5	chr12:9436248-9436298	RPTEC	kidney:	n/a
6	chr12:9436242-9436292	AG09309	skin:	n/a
7	chr12:9436242-9436292	NB4	blood:	n/a
8	chr12:9436248-9436298	PrEC	prostate:	n/a
9	chr12:9436242-9436292	RPTEC	kidney:	n/a
10	chr12:9436248-9436298	NB4	blood:	n/a
11	chr12:9436248-9436298	HUVEC	blood vessel:	n/a
12	chr12:9436248-9436298	Hepatocyte	liver:	n/a
13	chr12:9436248-9436298	BJ	skin:	n/a
14	chr12:9436242-9436292	NHBE	bronchial:	n/a
15	chr12:9436242-9436292	HEEpiC	esophagus:	n/a
16	chr12:9436248-9436298	IMR90	lung:	fetal
17	chr12:9436242-9436292	ovcar-3	ovarian:	n/a
18	chr12:9436242-9436292	MCF-7	breast:	n/a
19	chr12:9436242-9436292	SAEC	small airway:	n/a
20	chr12:9436248-9436298	ProgFib	skin:	n/a
21	chr12:9436248-9436298	HCM	heart:	n/a
22	chr12:9436242-9436292	HPAEpiC	pulmonary alveolar:	n/a
23	chr12:9436248-9436298	HRPEpiC	eye:	n/a
24	chr12:9436242-9436292	HEK293	kidney:	embryo
25	chr12:9436248-9436298	GM12891	blood:	n/a
26	chr12:9436248-9436298	HCT-116	colon:	n/a
27	chr12:9436242-9436292	GM06990	blood:	n/a
28	chr12:9436242-9436292	H1-hESC	embryonic stem cell:	embryo
29	chr12:9436242-9436292	HCT-116	colon:	n/a
30	chr12:9436248-9436298	ovcar-3	ovarian:	n/a
31	chr12:9436248-9436298	CMK	blood:	n/a
32	chr12:9436248-9436298	HRE	kidney:	n/a
33	chr12:9436242-9436292	U87	brain:	n/a
34	chr12:9436242-9436292	AG04449	skin:	fetal
35	chr12:9436242-9436292	SKMC	muscle:	n/a
36	chr12:9436248-9436298	AG04450	lung:	fetal
37	chr12:9436248-9436298	HepG2	liver:	n/a
38	chr12:9436248-9436298	GM12878	blood:	n/a
39	chr12:9436248-9436298	MCF10A-Er-Src	breast:	n/a
40	chr12:9436242-9436292	HUVEC	blood vessel:	n/a
41	chr12:9436242-9436292	A549	lung:	n/a
42	chr12:9436248-9436298	ECC-1	luminal epithelium:	n/a
43	chr12:9436242-9436292	LNCaP	prostate:	n/a
44	chr12:9436242-9436292	GM12891	blood:	n/a
45	chr12:9436242-9436292	AG09319	gingival:	n/a
46	chr12:9436242-9436292	HRE	kidney:	n/a
47	chr12:9436248-9436298	HAEpiC	amniotic membrane:	n/a
48	chr12:9436242-9436292	T-47D	breast:	n/a
49	chr12:9436248-9436298	HCF	heart:	n/a
50	chr12:9436248-9436298	A549	lung:	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	chr12:9436222..9437012-chr17:48045663..48046428,2	NB4	blood:
4	chr12:9435913..9436700-chr12:31226425..31227148,3	HCT-116	colon:
5	chr12:9436173..9436735-chr12:31226434..31227168,3	Hela-S3	cervix:
6	chr12:9436150..9437103-chr12:9600374..9601086,2	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000111788	TF binding region
ENSG00000111788	CpG island
ENSG00000108813	Chromatin interaction
ENSG00000214826	Chromatin interaction
ENSG00000013573	Chromatin interaction
ENSG00000256069	Chromatin interaction
ENSG00000111788	Chromatin interaction
ENSG00000245614	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10771445	0.81[EUR][1000 genomes]
rs10843242	0.82[EUR][1000 genomes]
rs10843243	0.82[EUR][1000 genomes]
rs10843244	0.82[EUR][1000 genomes]
rs11611191	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12581534	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12815281	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12816390	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12824461	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs187536	0.82[EUR][1000 genomes]
rs194037	0.82[EUR][1000 genomes]
rs252027	0.82[EUR][1000 genomes]
rs252028	0.82[EUR][1000 genomes]
rs252029	0.82[EUR][1000 genomes]
rs252030	0.82[EUR][1000 genomes]
rs252032	0.82[EUR][1000 genomes]
rs252033	0.82[EUR][1000 genomes]
rs34856550	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4883226	0.83[EUR][1000 genomes]
rs55913537	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56288591	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61916195	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7316531	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7967738	0.83[EUR][1000 genomes]
rs7980256	0.83[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
rs12822417	DDX12P	cis	Thyroid	GTEx
rs12822417	RP11-22B23.1	cis	Muscle Skeletal	GTEx
rs12822417	DDX12P	cis	Muscle Skeletal	GTEx
rs12822417	DDX12P	cis	Artery Tibial	GTEx
rs12822417	RP11-22B23.1	cis	Thyroid	GTEx
rs12822417	RP11-22B23.1	cis	Nerve Tibial	GTEx
rs12822417	A2MP1	cis	Adipose Subcutaneous	GTEx
rs12822417	RP11-22B23.1	cis	Skin Sun Exposed Lower leg	GTEx
rs12822417	A2MP1	cis	Nerve Tibial	GTEx
rs12822417	DDX12P	cis	Nerve Tibial	GTEx
rs12822417	RP11-22B23.1	cis	Artery Tibial	GTEx
rs12822417	RP11-22B23.1	cis	Whole Blood	GTEx
rs12822417	RP11-22B23.1	cis	lung	GTEx

Chromatin state (count:116 , 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	chr12:9435400-9436400	Enhancers	Hela-S3	cervix
3	chr12:9435400-9437800	Active TSS	A549	lung
4	chr12:9435400-9464000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr12:9435600-9436400	Active TSS	Primary T cells from cord blood	blood
6	chr12:9435600-9437800	Active TSS	Primary hematopoietic stem cells short term culture	blood
7	chr12:9435600-9437800	Active TSS	GM12878-XiMat	blood
8	chr12:9435800-9436400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr12:9435800-9436400	Active TSS	Monocytes-CD14+_RO01746	blood
10	chr12:9435800-9436600	Active TSS	Primary T killer memory cells from peripheral blood	blood
11	chr12:9435800-9437000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr12:9435800-9437000	Active TSS	Primary T helper cells fromperipheralblood	blood
13	chr12:9435800-9437000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
14	chr12:9435800-9437000	Active TSS	Brain Anterior Caudate	brain
15	chr12:9435800-9437000	Active TSS	Brain Inferior Temporal Lobe	brain
16	chr12:9435800-9437000	Active TSS	Stomach Smooth Muscle	stomach
17	chr12:9435800-9437200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr12:9435800-9437200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr12:9435800-9437200	Active TSS	Brain Substantia Nigra	brain
20	chr12:9435800-9437200	Active TSS	Duodenum Smooth Muscle	Duodenum
21	chr12:9435800-9437200	Active TSS	NHDF-Ad	bronchial
22	chr12:9435800-9437400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
23	chr12:9435800-9437400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr12:9435800-9437400	Active TSS	Fetal Brain Female	brain
25	chr12:9435800-9437600	Active TSS	HUES48 Cell Line	embryonic stem cell
26	chr12:9435800-9437600	Active TSS	Rectal Mucosa Donor 29	rectum
27	chr12:9435800-9437800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr12:9435800-9437800	Active TSS	iPS-15b Cell Line	embryonic stem cell
29	chr12:9435800-9437800	Active TSS	iPS-20b Cell Line	embryonic stem cell
30	chr12:9435800-9437800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr12:9435800-9437800	Active TSS	K562	blood
32	chr12:9436000-9436400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr12:9436000-9436400	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr12:9436000-9436400	Active TSS	Colon Smooth Muscle	Colon
35	chr12:9436000-9436400	Active TSS	Fetal Muscle Leg	muscle
36	chr12:9436000-9436400	Active TSS	Fetal Thymus	thymus
37	chr12:9436000-9436400	Active TSS	Psoas Muscle	Psoas
38	chr12:9436000-9436400	Active TSS	Right Ventricle	heart
39	chr12:9436000-9436400	Active TSS	Thymus	Thymus
40	chr12:9436000-9436400	Active TSS	HSMM	muscle
41	chr12:9436000-9436400	Active TSS	HSMMtube	muscle
42	chr12:9436000-9436600	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
43	chr12:9436000-9436800	Active TSS	Placenta	Placenta
44	chr12:9436000-9437000	Active TSS	Primary monocytes fromperipheralblood	blood
45	chr12:9436000-9437000	Active TSS	Primary B cells from cord blood	blood
46	chr12:9436000-9437000	Active TSS	Primary B cells from peripheral blood	blood
47	chr12:9436000-9437000	Active TSS	Primary T cells fromperipheralblood	blood
48	chr12:9436000-9437000	Active TSS	Primary hematopoietic stem cells	blood
49	chr12:9436000-9437000	Active TSS	Primary T helper naive cells from peripheral blood	blood
50	chr12:9436000-9437000	Active TSS	Primary T killer naive cells fromperipheralblood	blood

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