Variant report

Variant	rs1716169
Chromosome Location	chr12:123716930-123716931
allele	A/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	MXI1	chr12:123716346-123718916	IMR90	lung:	n/a	n/a
2	POLR2A	chr12:123716754-123718431	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr12:123716616-123718302	PFSK-1	brain:	n/a	n/a
4	NR2F2	chr12:123716903-123719098	K562	blood:	n/a	n/a
5	REST	chr12:123716397-123718706	H1-neurons	neurons:	n/a	chr12:123717783-123717796 chr12:123717593-123717603 chr12:123717449-123717462
6	EBF1	chr12:123716549-123718110	GM12878	blood:	n/a	chr12:123716736-123716745
7	POLR2A	chr12:123716927-123718306	HUVEC	blood vessel:	n/a	n/a
8	E2F6	chr12:123716916-123718498	A549	lung:	n/a	chr12:123717981-123717990 chr12:123717717-123717726 chr12:123717865-123717874 chr12:123717434-123717441
9	SIN3A	chr12:123716688-123718537	H1-hESC	embryonic stem cell:	n/a	chr12:123717449-123717462 chr12:123718440-123718448 chr12:123718285-123718293 chr12:123717783-123717796
10	MTA3	chr12:123716877-123718956	GM12878	blood:	n/a	n/a
11	ATF3	chr12:123716799-123717823	A549	lung:	n/a	chr12:123717501-123717515 chr12:123717694-123717703
12	POLR2A	chr12:123716426-123718453	HepG2	liver:	n/a	n/a
13	POLR2A	chr12:123716925-123718396	MCF10A-Er-Src	breast:	n/a	n/a
14	MAX	chr12:123716927-123718665	A549	lung:	n/a	n/a
15	TCF12	chr12:123716688-123718420	A549	lung:	n/a	chr12:123717931-123717940
16	POLR2A	chr12:123716917-123718785	GM12892	blood:	n/a	n/a
17	RCOR1	chr12:123716685-123718459	Hela-S3	cervix:	n/a	n/a
18	NFYA	chr12:123716924-123718171	Hela-S3	cervix:	n/a	chr12:123717862-123717876 chr12:123717716-123717726 chr12:123717488-123717502 chr12:123717864-123717874 chr12:123717861-123717876 chr12:123717713-123717728 chr12:123717857-123717875 chr12:123717861-123717876 chr12:123717715-123717728 chr12:123717713-123717728
19	POLR2A	chr12:123716929-123718394	U87	brain:	n/a	n/a
20	TBP	chr12:123716681-123718384	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr12:123716889-123718531	PFSK-1	brain:	n/a	n/a
22	POLR2A	chr12:123716882-123718522	H1-hESC	embryonic stem cell:	n/a	n/a
23	SP1	chr12:123716928-123718348	A549	lung:	n/a	chr12:123718229-123718238 chr12:123717365-123717374 chr12:123717364-123717378 chr12:123717833-123717845 chr12:123717833-123717845 chr12:123717489-123717510 chr12:123717854-123717875 chr12:123717363-123717375 chr12:123717363-123717375 chr12:123717730-123717744 chr12:123717364-123717373 chr12:123717834-123717843
24	POLR2A	chr12:123716531-123718440	GM12891	blood:	n/a	n/a
25	MAZ	chr12:123716615-123718801	IMR90	lung:	n/a	n/a
26	FOXM1	chr12:123716897-123718227	GM12878	blood:	n/a	n/a
27	SP1	chr12:123716923-123718571	A549	lung:	n/a	chr12:123718229-123718238 chr12:123717365-123717374 chr12:123717364-123717378 chr12:123717833-123717845 chr12:123717833-123717845 chr12:123717489-123717510 chr12:123717854-123717875 chr12:123717363-123717375 chr12:123717363-123717375 chr12:123717730-123717744 chr12:123717364-123717373 chr12:123717834-123717843
28	RFX5	chr12:123716688-123718221	Hela-S3	cervix:	n/a	chr12:123717491-123717500 chr12:123717716-123717725 chr12:123717864-123717873
29	MXI1	chr12:123716350-123718974	SK-N-SH	brain:	n/a	n/a
30	PBX3	chr12:123716928-123718166	SK-N-SH	brain:	n/a	chr12:123717051-123717062 chr12:123717864-123717873 chr12:123717491-123717500 chr12:123717394-123717414
31	HCFC1	chr12:123716685-123718970	Hela-S3	cervix:	n/a	n/a
32	SIN3AK20	chr12:123716827-123718648	MCF-7	breast:	n/a	n/a
33	REST	chr12:123716554-123718537	A549	lung:	n/a	chr12:123717783-123717796 chr12:123717593-123717603 chr12:123717449-123717462
34	POLR2A	chr12:123716835-123718394	U87	brain:	n/a	n/a
35	STAT3	chr12:123716871-123717045	MCF10A-Er-Src	breast:	n/a	n/a
36	POLR2A	chr12:123716906-123718310	HepG2	liver:	n/a	n/a
37	EP300	chr12:123716897-123718170	GM12878	blood:	n/a	n/a
38	SP1	chr12:123716892-123718522	HCT-116	colon:	n/a	chr12:123718229-123718238 chr12:123717365-123717374 chr12:123717364-123717378 chr12:123717833-123717845 chr12:123717833-123717845 chr12:123717489-123717510 chr12:123717854-123717875 chr12:123717363-123717375 chr12:123717363-123717375 chr12:123717730-123717744 chr12:123717364-123717373 chr12:123717834-123717843
39	RELA	chr12:123716787-123718396	GM18505	blood:	n/a	n/a
40	MYBL2	chr12:123716926-123718310	HepG2	liver:	n/a	n/a
41	CHD2	chr12:123716918-123718341	Hela-S3	cervix:	n/a	chr12:123717434-123717441
42	POLR2A	chr12:123716873-123718657	PANC-1	pancreas:	n/a	n/a
43	POLR2A	chr12:123716397-123718693	SK-N-MC	brain:	n/a	n/a
44	TAF1	chr12:123716834-123718488	ECC-1	luminal epithelium:	n/a	n/a
45	GATA1	chr12:123716297-123719103	K562	blood:	n/a	chr12:123717946-123717967 chr12:123717953-123717960 chr12:123717953-123717960 chr12:123716547-123716557 chr12:123717953-123717960
46	POLR2A	chr12:123716888-123718824	HepG2	liver:	n/a	n/a
47	ZNF263	chr12:123716441-123718758	HEK293-T-REx	kidney:	n/a	chr12:123718673-123718682
48	MAX	chr12:123716901-123718773	Hela-S3	cervix:	n/a	n/a
49	MAX	chr12:123716896-123718668	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:123344301..123346489-chr12:123716077..123720315,3	K562	blood:
2	chr12:123716171..123718231-chr12:124086645..124088616,2	K562	blood:
3	chr12:123634123..123636368-chr12:123714378..123717139,2	MCF-7	breast:
4	chr12:123465881..123468570-chr12:123716034..123719414,3	K562	blood:
5	chr12:123377844..123381497-chr12:123716230..123718980,3	K562	blood:
6	chr12:123458067..123461017-chr12:123715728..123717607,2	MCF-7	breast:
7	chr12:123348260..123351060-chr12:123715794..123718322,2	K562	blood:
8	chr12:123715622..123719446-chr12:123735072..123738647,4	K562	blood:
9	chr12:123633130..123634910-chr12:123716201..123717715,2	K562	blood:
10	chr12:123478491..123480718-chr12:123715406..123717168,2	MCF-7	breast:
11	chr12:123593239..123596148-chr12:123716066..123718804,3	K562	blood:
12	chr12:123714199..123721299-chr12:123733822..123739052,7	MCF-7	breast:
13	chr12:123646433..123649058-chr12:123716040..123717583,2	MCF-7	breast:
14	chr12:123716817..123718990-chr12:124117809..124119418,3	K562	blood:
15	chr12:123716801..123717680-chr3:168863866..168864454,2	Hela-S3	cervix:
16	chr12:123457894..123461734-chr12:123715409..123718960,7	K562	blood:
17	chr12:52446813..52447635-chr12:123716880..123717854,2	Hela-S3	cervix:
18	chr12:123715746..123718967-chr12:123870796..123875270,4	K562	blood:
19	chr12:123704862..123707251-chr12:123716101..123718102,3	MCF-7	breast:
20	chr12:123463210..123468211-chr12:123716151..123721062,7	MCF-7	breast:
21	chr12:123715079..123721002-chr12:123721919..123730378,16	K562	blood:
22	chr12:123716880..123717788-chr19:50369332..50370290,2	Hela-S3	cervix:
23	chr12:123459054..123462367-chr12:123715409..123720380,5	K562	blood:
24	chr12:123716636..123719469-chr12:124192807..124195608,2	K562	blood:
25	chr12:123716734..123718943-chr12:124067701..124069242,2	MCF-7	breast:
26	chr12:123716549..123717256-chr19:49956441..49956976,2	Hela-S3	cervix:
27	chr12:123558968..123563276-chr12:123716606..123719909,6	MCF-7	breast:
28	chr12:123715831..123718104-chr12:123754466..123757204,4	MCF-7	breast:
29	chr12:123449701..123452611-chr12:123716445..123719411,3	K562	blood:
30	chr12:123474497..123476026-chr12:123715304..123717447,2	K562	blood:
31	chr12:123449477..123453379-chr12:123715163..123718004,4	MCF-7	breast:
32	chr12:123458147..123462549-chr12:123715608..123720287,8	MCF-7	breast:
33	chr12:123380300..123383026-chr12:123716228..123718007,3	K562	blood:
34	chr12:123716353..123719935-chr12:123753594..123757800,6	K562	blood:

Variant related genes	Relation type
MPHOSPH9	TF binding region
C12orf65	TF binding region
ENSG00000090975	Chromatin interaction
ENSG00000039650	Chromatin interaction
ENSG00000111361	Chromatin interaction
ENSG00000111325	Chromatin interaction
ENSG00000256152	Chromatin interaction
ENSG00000051825	Chromatin interaction
ENSG00000123358	Chromatin interaction
ENSG00000086598	Chromatin interaction
ENSG00000085276	Chromatin interaction
ENSG00000130921	Chromatin interaction
ENSG00000111358	Chromatin interaction
ENSG00000255839	Chromatin interaction
ENSG00000111364	Chromatin interaction
ENSG00000104872	Chromatin interaction
ENSG00000161618	Chromatin interaction
ENSG00000150967	Chromatin interaction
ENSG00000182196	Chromatin interaction
ENSG00000139722	Chromatin interaction
ENSG00000256028	Chromatin interaction
ENSG00000111328	Chromatin interaction
ENSG00000183955	Chromatin interaction
ENSG00000130787	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10772998	0.82[EUR][1000 genomes]
rs10846487	0.83[EUR][1000 genomes]
rs11057204	0.81[EUR][1000 genomes]
rs11057206	0.81[EUR][1000 genomes]
rs12817892	0.84[EUR][1000 genomes]
rs12818067	0.84[EUR][1000 genomes]
rs12829456	0.84[EUR][1000 genomes]
rs1716170	0.83[EUR][1000 genomes]
rs1716171	0.83[EUR][1000 genomes]
rs1716172	0.82[EUR][1000 genomes]
rs1727322	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1727334	0.83[EUR][1000 genomes]
rs2695480	0.82[AMR][1000 genomes]
rs2851435	0.81[EUR][1000 genomes]
rs34341465	0.84[EUR][1000 genomes]
rs58809476	0.84[EUR][1000 genomes]
rs941305	0.83[EUR][1000 genomes]
rs941306	0.83[EUR][1000 genomes]
rs9795522	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	esv1803368	chr12:123640853-123822503	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
6	esv1830566	chr12:123640853-123822503	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
7	esv1836043	chr12:123709409-123822503	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1716169	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL
rs1716169	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs1716169	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs1716169	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs1716169	CDK2AP1	cis	Skin Sun Exposed Lower leg	GTEx
rs1716169	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs1716169	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123687800-123717000	Weak transcription	Aorta	Aorta
2	chr12:123706800-123717000	Weak transcription	Small Intestine	intestine
3	chr12:123715200-123717200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr12:123715600-123717000	Flanking Active TSS	Dnd41	blood
5	chr12:123716000-123717000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr12:123716000-123717200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
7	chr12:123716000-123717200	Flanking Active TSS	Liver	Liver
8	chr12:123716200-123717000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr12:123716200-123717000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
10	chr12:123716200-123717000	Flanking Active TSS	Brain Germinal Matrix	brain
11	chr12:123716200-123717200	Flanking Active TSS	Primary T cells from cord blood	blood
12	chr12:123716200-123717200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr12:123716200-123717200	Flanking Active TSS	HUVEC	blood vessel
14	chr12:123716200-123717400	Flanking Active TSS	Primary B cells from cord blood	blood
15	chr12:123716200-123718400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:123716200-123719000	Active TSS	ES-I3 Cell Line	embryonic stem cell
17	chr12:123716200-123719400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr12:123716200-123719400	Active TSS	GM12878-XiMat	blood
19	chr12:123716200-123719800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr12:123716400-123717000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr12:123716400-123717000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
22	chr12:123716400-123717000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
23	chr12:123716400-123717000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr12:123716400-123717000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr12:123716400-123717000	Flanking Active TSS	Brain Angular Gyrus	brain
26	chr12:123716400-123717000	Flanking Active TSS	Brain Hippocampus Middle	brain
27	chr12:123716400-123717000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
28	chr12:123716400-123717000	Flanking Active TSS	Colon Smooth Muscle	Colon
29	chr12:123716400-123717000	Flanking Active TSS	Duodenum Mucosa	Duodenum
30	chr12:123716400-123717000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
31	chr12:123716400-123717000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
32	chr12:123716400-123717000	Flanking Active TSS	Fetal Brain Male	brain
33	chr12:123716400-123717000	Flanking Active TSS	Fetal Heart	heart
34	chr12:123716400-123717000	Flanking Active TSS	Fetal Lung	lung
35	chr12:123716400-123717000	Flanking Active TSS	Fetal Muscle Leg	muscle
36	chr12:123716400-123717000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
37	chr12:123716400-123717000	Flanking Active TSS	Right Ventricle	heart
38	chr12:123716400-123717000	Enhancers	Sigmoid Colon	Sigmoid Colon
39	chr12:123716400-123717000	Flanking Active TSS	Thymus	Thymus
40	chr12:123716400-123717000	Flanking Active TSS	NHEK	skin
41	chr12:123716400-123717000	Flanking Active TSS	Osteobl	bone
42	chr12:123716400-123717200	Flanking Active TSS	Primary hematopoietic stem cells	blood
43	chr12:123716400-123717200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
44	chr12:123716400-123717200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
45	chr12:123716400-123717200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
46	chr12:123716400-123717200	Flanking Active TSS	Adipose Nuclei	Adipose
47	chr12:123716400-123717200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
48	chr12:123716400-123717400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
49	chr12:123716400-123718600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr12:123716400-123718800	Active TSS	H9 Cell Line	embryonic stem cell

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