Variant report

Variant	rs1716183
Chromosome Location	chr12:123635096-123635097
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	RAD21	chr12:123634918-123636290	IMR90	lung:	n/a	chr12:123635261-123635274
2	YY1	chr12:123634704-123635232	HepG2	liver:	n/a	chr12:123634955-123634966
3	HA-E2F1	chr12:123634958-123635928	Hela-S3	cervix:	n/a	chr12:123635154-123635164 chr12:123635884-123635893 chr12:123635879-123635889 chr12:123635755-123635764 chr12:123635494-123635504
4	POLR2A	chr12:123634877-123635180	H1-neurons	neurons:	n/a	n/a
5	UBTF	chr12:123634016-123635929	K562	blood:	n/a	n/a
6	CCNT2	chr12:123634810-123636248	K562	blood:	n/a	chr12:123634810-123634819
7	E2F6	chr12:123634714-123635201	K562	blood:	n/a	chr12:123634869-123634881 chr12:123635154-123635164
8	MAX	chr12:123634385-123635947	A549	lung:	n/a	chr12:123635502-123635517 chr12:123635004-123635011 chr12:123635756-123635766 chr12:123635000-123635009
9	GATA1	chr12:123632620-123635248	K562	blood:	n/a	n/a
10	MAX	chr12:123634811-123635188	ECC-1	luminal epithelium:	n/a	chr12:123635004-123635011 chr12:123635000-123635009
11	E2F6	chr12:123634835-123635861	K562	blood:	n/a	chr12:123634869-123634881 chr12:123635154-123635164 chr12:123635755-123635764 chr12:123635494-123635504
12	POLR2A	chr12:123634850-123637088	K562	blood:	n/a	n/a
13	CTCF	chr12:123634644-123636349	SK-N-SH	brain:	n/a	chr12:123635144-123635157 chr12:123636264-123636273
14	ZBTB7A	chr12:123634598-123635237	ECC-1	luminal epithelium:	n/a	chr12:123634780-123634789
15	POLR2A	chr12:123634923-123635196	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr12:123635013-123635156	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr12:123634888-123635418	HUVEC	blood vessel:	n/a	n/a
18	UBTF	chr12:123633939-123636396	K562	blood:	n/a	n/a
19	POLR2A	chr12:123634860-123635157	A549	lung:	n/a	n/a
20	MYC	chr12:123634952-123635096	K562	blood:	n/a	chr12:123635004-123635011 chr12:123635000-123635009
21	POLR2A	chr12:123634935-123636356	HUVEC	blood vessel:	n/a	n/a
22	POLR2A	chr12:123634894-123635142	HepG2	liver:	n/a	n/a
23	SMARCB1	chr12:123634476-123635327	Hela-S3	cervix:	n/a	n/a
24	ZBTB7A	chr12:123634326-123635981	K562	blood:	n/a	chr12:123634780-123634789
25	ZBTB7A	chr12:123634603-123635347	ECC-1	luminal epithelium:	n/a	chr12:123634780-123634789
26	MAX	chr12:123634713-123636081	K562	blood:	n/a	chr12:123635502-123635517 chr12:123635004-123635011 chr12:123635756-123635766 chr12:123635000-123635009
27	POLR2A	chr12:123635003-123635991	A549	lung:	n/a	n/a
28	MXI1	chr12:123634450-123636293	IMR90	lung:	n/a	n/a
29	MAZ	chr12:123635013-123635849	K562	blood:	n/a	chr12:123635502-123635517 chr12:123635756-123635766
30	MAX	chr12:123634993-123635826	Hela-S3	cervix:	n/a	chr12:123635502-123635517 chr12:123635004-123635011 chr12:123635756-123635766 chr12:123635000-123635009
31	SIN3A	chr12:123634685-123635188	H1-hESC	embryonic stem cell:	n/a	n/a
32	MAX	chr12:123634264-123636428	A549	lung:	n/a	chr12:123635502-123635517 chr12:123635004-123635011 chr12:123635756-123635766 chr12:123635000-123635009
33	NFIC	chr12:123634811-123635302	ECC-1	luminal epithelium:	n/a	n/a
34	POLR2A	chr12:123635082-123635167	MCF-7	breast:	n/a	n/a
35	POLR2A	chr12:123634951-123635278	HCT-116	colon:	n/a	n/a
36	POLR2A	chr12:123634930-123635392	HUVEC	blood vessel:	n/a	n/a
37	MAZ	chr12:123634723-123636549	IMR90	lung:	n/a	chr12:123635502-123635517 chr12:123635004-123635011 chr12:123635756-123635766 chr12:123635000-123635009
38	POLR2A	chr12:123634925-123635123	K562	blood:	n/a	n/a
39	POLR2A	chr12:123634307-123636312	A549	lung:	n/a	n/a
40	POLR2A	chr12:123635094-123635715	K562	blood:	n/a	n/a
41	MAX	chr12:123634319-123636247	HepG2	liver:	n/a	chr12:123635502-123635517 chr12:123635004-123635011 chr12:123635756-123635766 chr12:123635000-123635009
42	E2F6	chr12:123634685-123635745	H1-hESC	embryonic stem cell:	n/a	chr12:123634869-123634881 chr12:123635154-123635164 chr12:123635494-123635504
43	ZNF263	chr12:123633201-123635347	HEK293-T-REx	kidney:	n/a	chr12:123635122-123635131 chr12:123634374-123634395
44	HMGN3	chr12:123634697-123636305	K562	blood:	n/a	n/a
45	CTCF	chr12:123634960-123635110	AG04449	skin:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:123634064..123637299-chr12:123639365..123644376,5	K562	blood:
2	chr12:123552676..123554200-chr12:123634961..123636565,2	K562	blood:
3	chr12:123527678..123528658-chr12:123634881..123635709,3	MCF-7	breast:
4	chr12:123517171..123520609-chr12:123634791..123638617,3	K562	blood:
5	chr12:123617700..123620555-chr12:123634870..123636855,3	MCF-7	breast:
6	chr12:123575945..123576658-chr12:123634764..123635731,2	K562	blood:
7	chr12:123634768..123637262-chr12:124085657..124088192,2	K562	blood:
8	chr12:123318440..123320805-chr12:123633475..123636263,2	MCF-7	breast:
9	chr12:123461071..123463448-chr12:123634660..123637484,2	K562	blood:
10	chr12:123634123..123636368-chr12:123714378..123717139,2	MCF-7	breast:
11	chr12:123574871..123577625-chr12:123635000..123637260,3	MCF-7	breast:
12	chr12:123634522..123637208-chr12:123639726..123642249,4	K562	blood:
13	chr12:123314439..123317163-chr12:123634963..123637139,2	K562	blood:
14	chr12:123634053..123636860-chr12:123645111..123649875,5	MCF-7	breast:
15	chr12:123633368..123635688-chr12:123701614..123704544,2	MCF-7	breast:
16	chr12:123634793..123637876-chr12:123640152..123646460,6	MCF-7	breast:
17	chr12:123526656..123529148-chr12:123634939..123636869,3	MCF-7	breast:
18	chr12:123463900..123466022-chr12:123633750..123636695,4	K562	blood:
19	chr12:123463900..123467066-chr12:123633750..123636695,4	K562	blood:
20	chr12:123540726..123542900-chr12:123635050..123636986,3	MCF-7	breast:
21	chr12:123588003..123590511-chr12:123634129..123636612,2	MCF-7	breast:

Variant related genes	Relation type
PITPNM2	TF binding region
ENSG00000111325	Chromatin interaction
ENSG00000150967	Chromatin interaction
ENSG00000051825	Chromatin interaction
ENSG00000090975	Chromatin interaction
ENSG00000130787	Chromatin interaction
ENSG00000111364	Chromatin interaction
ENSG00000182196	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1047158	0.93[ASN][1000 genomes]
rs1051431	0.93[ASN][1000 genomes]
rs10772993	0.93[ASN][1000 genomes]
rs1106240	0.93[ASN][1000 genomes]
rs1106241	0.93[ASN][1000 genomes]
rs1569068	0.93[ASN][1000 genomes]
rs1616131	0.93[ASN][1000 genomes]
rs1616181	0.93[ASN][1000 genomes]
rs1617434	0.93[ASN][1000 genomes]
rs1618679	0.81[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1621194	0.81[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1627724	0.81[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1716165	0.93[ASN][1000 genomes]
rs1716167	0.93[ASN][1000 genomes]
rs1716168	0.81[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1716185	0.93[ASN][1000 genomes]
rs1727296	0.87[ASN][1000 genomes]
rs1727313	0.93[ASN][1000 genomes]
rs1727314	0.93[ASN][1000 genomes]
rs1727315	0.81[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1727316	0.93[ASN][1000 genomes]
rs1727317	0.93[ASN][1000 genomes]
rs1790090	0.93[ASN][1000 genomes]
rs1790108	0.81[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1790109	0.81[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1790116	0.93[ASN][1000 genomes]
rs2682429	0.93[ASN][1000 genomes]
rs2695481	0.93[ASN][1000 genomes]
rs2695482	0.93[ASN][1000 genomes]
rs2851438	0.93[ASN][1000 genomes]
rs884548	0.93[ASN][1000 genomes]
rs949142	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3388790	chr12:123275902-123655103	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv517200	chr12:123312051-123654498	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv427924	chr12:123412172-123722059	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
4	nsv1042550	chr12:123532028-123659500	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	esv1825473	chr12:123582855-123822503	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
6	nsv870326	chr12:123585990-123719323	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
7	esv2761773	chr12:123616003-123723460	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
8	esv3439435	chr12:123634349-123637047	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	esv3440997	chr12:123634424-123637372	Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1716183	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL
rs1716183	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs1716183	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs1716183	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL
rs1716183	LOC283378	Cis_1M	lymphoblastoid	RTeQTL
rs1716183	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs1716183	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123633800-123635200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
2	chr12:123633800-123635200	Flanking Active TSS	Stomach Smooth Muscle	stomach
3	chr12:123633800-123636000	Active TSS	Brain Inferior Temporal Lobe	brain
4	chr12:123633800-123636200	Active TSS	NHLF	lung
5	chr12:123633800-123636400	Active TSS	Brain Cingulate Gyrus	brain
6	chr12:123633800-123636600	Active TSS	Duodenum Smooth Muscle	Duodenum
7	chr12:123634000-123635200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
8	chr12:123634000-123635200	Flanking Active TSS	Primary B cells from cord blood	blood
9	chr12:123634000-123635200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
10	chr12:123634000-123635200	Flanking Bivalent TSS/Enh	Dnd41	blood
11	chr12:123634000-123636000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
12	chr12:123634000-123636400	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr12:123634200-123636400	Active TSS	Brain Anterior Caudate	brain
14	chr12:123634400-123635200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
15	chr12:123634400-123635200	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
16	chr12:123634400-123635200	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
17	chr12:123634400-123635200	Flanking Active TSS	Primary hematopoietic stem cells	blood
18	chr12:123634400-123635200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
19	chr12:123634400-123635200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr12:123634400-123636000	Weak transcription	Fetal Kidney	kidney
21	chr12:123634400-123636200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
22	chr12:123634400-123636200	Active TSS	Rectal Smooth Muscle	rectum
23	chr12:123634400-123636400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr12:123634400-123636400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
25	chr12:123634400-123636600	Active TSS	Colon Smooth Muscle	Colon
26	chr12:123634600-123635200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
27	chr12:123634600-123635200	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
28	chr12:123634600-123635200	Flanking Active TSS	Placenta	Placenta
29	chr12:123634600-123635200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
30	chr12:123634600-123636000	Active TSS	Primary T cells from cord blood	blood
31	chr12:123634600-123636200	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr12:123634600-123636200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr12:123634600-123636200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr12:123634600-123636200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
35	chr12:123634600-123636200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr12:123634600-123636200	Active TSS	Brain Angular Gyrus	brain
37	chr12:123634600-123636200	Active TSS	Gastric	stomach
38	chr12:123634600-123636200	Active TSS	Small Intestine	intestine
39	chr12:123634600-123636200	Active TSS	A549	lung
40	chr12:123634600-123636200	Active TSS	Hela-S3	cervix
41	chr12:123634600-123636200	Active TSS	NHDF-Ad	bronchial
42	chr12:123634600-123636400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr12:123634600-123636400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
44	chr12:123634600-123636400	Active TSS	Aorta	Aorta
45	chr12:123634600-123636400	Active TSS	Left Ventricle	heart
46	chr12:123634600-123636400	Active TSS	Ovary	ovary
47	chr12:123634600-123636600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr12:123634800-123635200	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr12:123634800-123635200	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
50	chr12:123634800-123635200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood

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