Variant report

Variant	rs35325227
Chromosome Location	chr12:105724965-105724966
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	EGR1	chr12:105724750-105725016	GM12878	blood:	n/a	chr12:105724940-105724950 chr12:105724885-105724898 chr12:105724887-105724897 chr12:105724888-105724897 chr12:105724886-105724900 chr12:105724885-105724898 chr12:105724885-105724899 chr12:105724885-105724898 chr12:105724885-105724898
2	CTCF	chr12:105724920-105725070	SAEC	small airway:	n/a	n/a
3	ZNF143	chr12:105724203-105725131	GM12878	blood:	n/a	chr12:105724298-105724316 chr12:105724274-105724284
4	MXI1	chr12:105723677-105726002	IMR90	lung:	n/a	chr12:105724251-105724260
5	PAX5	chr12:105724177-105725015	GM12892	blood:	n/a	n/a
6	RAD21	chr12:105724778-105724974	SK-N-SH_RA	brain:	n/a	n/a
7	CTCF	chr12:105724860-105725010	NHEK	skin:	n/a	chr12:105724884-105724897
8	POLR2A	chr12:105723741-105725429	GM18526	blood:	n/a	n/a
9	MAX	chr12:105723778-105725315	A549	lung:	n/a	n/a
10	CTCF	chr12:105724811-105724996	MCF-7	breast:	n/a	chr12:105724884-105724897
11	CTCF	chr12:105724824-105724971	GM12891	blood:	n/a	chr12:105724884-105724897
12	MYC	chr12:105724846-105724997	MCF-7	breast:	n/a	n/a
13	CTCF	chr12:105724799-105724989	GM12892	blood:	n/a	chr12:105724884-105724897
14	POLR2A	chr12:105724922-105725839	SK-N-SH	brain:	n/a	n/a
15	SIN3AK20	chr12:105724791-105725340	SK-N-SH	brain:	n/a	n/a
16	SIN3AK20	chr12:105724743-105725098	PANC-1	pancreas:	n/a	n/a
17	CTCF	chr12:105724811-105725110	IMR90	lung:	n/a	chr12:105724884-105724897
18	CTCF	chr12:105724832-105724983	MCF-7	breast:	n/a	chr12:105724884-105724897
19	MAX	chr12:105724655-105725130	ECC-1	luminal epithelium:	n/a	n/a
20	CTCF	chr12:105724820-105724970	HUVEC	blood vessel:	n/a	chr12:105724884-105724897
21	ZNF263	chr12:105724760-105725348	HEK293-T-REx	kidney:	n/a	n/a
22	SIN3A	chr12:105724825-105726056	H1-hESC	embryonic stem cell:	n/a	n/a
23	MAZ	chr12:105723746-105725701	IMR90	lung:	n/a	n/a
24	CTCF	chr12:105724880-105725030	GM12875	blood:	n/a	chr12:105724884-105724897
25	TCF12	chr12:105724862-105725048	GM12878	blood:	n/a	n/a
26	EGR1	chr12:105724747-105725086	H1-hESC	embryonic stem cell:	n/a	chr12:105724940-105724950 chr12:105724885-105724898 chr12:105724887-105724897 chr12:105724888-105724897 chr12:105724886-105724900 chr12:105724885-105724898 chr12:105724885-105724899 chr12:105724885-105724898 chr12:105724885-105724898
27	SMC3	chr12:105724865-105725063	Hela-S3	cervix:	n/a	n/a
28	CTCF	chr12:105724880-105725030	HCFaa	heart:	n/a	chr12:105724884-105724897
29	RAD21	chr12:105724681-105725298	IMR90	lung:	n/a	n/a
30	ZEB1	chr12:105724786-105725143	GM12878	blood:	n/a	chr12:105725114-105725125 chr12:105724983-105724992
31	MAX	chr12:105723718-105725297	NB4	blood:	n/a	n/a
32	EGR1	chr12:105724532-105725173	HCT-116	colon:	n/a	chr12:105724940-105724950 chr12:105724885-105724898 chr12:105724887-105724897 chr12:105724888-105724897 chr12:105724886-105724900 chr12:105724885-105724898 chr12:105724885-105724899 chr12:105724885-105724898 chr12:105724885-105724898
33	CTCF	chr12:105724780-105725070	GM12868	blood:	n/a	chr12:105724884-105724897
34	MAX	chr12:105723720-105726217	A549	lung:	n/a	n/a
35	POLR2A	chr12:105723786-105725397	GM15510	blood:	n/a	n/a
36	CHD1	chr12:105724921-105725132	GM12878	blood:	n/a	n/a
37	EGR1	chr12:105724746-105724993	GM12878	blood:	n/a	chr12:105724940-105724950 chr12:105724885-105724898 chr12:105724887-105724897 chr12:105724888-105724897 chr12:105724886-105724900 chr12:105724885-105724898 chr12:105724885-105724899 chr12:105724885-105724898 chr12:105724885-105724898
38	POLR2A	chr12:105724884-105725091	A549	lung:	n/a	n/a
39	EGR1	chr12:105724753-105725053	K562	blood:	n/a	chr12:105724940-105724950 chr12:105724885-105724898 chr12:105724887-105724897 chr12:105724888-105724897 chr12:105724886-105724900 chr12:105724885-105724898 chr12:105724885-105724899 chr12:105724885-105724898 chr12:105724885-105724898
40	POLR2A	chr12:105723805-105726031	GM19099	blood:	n/a	n/a
41	BACH1	chr12:105724876-105725095	H1-hESC	embryonic stem cell:	n/a	n/a
42	TAF1	chr12:105724762-105724975	SK-N-SH	brain:	n/a	n/a
43	POLR2A	chr12:105724029-105724987	A549	lung:	n/a	n/a
44	SMARCB1	chr12:105724029-105725175	Hela-S3	cervix:	n/a	n/a
45	CTCF	chr12:105724840-105724990	HA-sp	spinal cord:	n/a	chr12:105724884-105724897
46	ZBTB7A	chr12:105723962-105725353	ECC-1	luminal epithelium:	n/a	chr12:105724287-105724294
47	CTCF	chr12:105724840-105724990	HMEC	breast:	n/a	chr12:105724884-105724897
48	MAZ	chr12:105724146-105725192	Hela-S3	cervix:	n/a	n/a
49	CTCF	chr12:105724814-105724987	MCF-7	breast:	n/a	chr12:105724884-105724897
50	EGR1	chr12:105724581-105725268	HCT-116	colon:	n/a	chr12:105724940-105724950 chr12:105724885-105724898 chr12:105724887-105724897 chr12:105724888-105724897 chr12:105724886-105724900 chr12:105724885-105724898 chr12:105724885-105724899 chr12:105724885-105724898 chr12:105724885-105724898

No.	Distal block	Cell Line	Cell type
1	chr12:105720223..105722150-chr12:105723159..105726102,2	MCF-7	breast:
2	chr12:105724066..105725047-chr3:25831350..25832040,2	NB4	blood:
3	chr12:105628750..105631438-chr12:105722608..105725285,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257642	TF binding region
ENSG00000264749	TF binding region
ENSG00000264749	Chromatin interaction
ENSG00000136044	Chromatin interaction
ENSG00000257642	Chromatin interaction
ENSG00000235162	Chromatin interaction
ENSG00000151093	Chromatin interaction
ENSG00000151092	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10861400	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10861403	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11112469	0.86[GIH][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11112470	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11112473	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11112475	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11112478	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11112480	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11112482	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11112483	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11112484	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11112485	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11112486	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11112487	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11112488	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12829692	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1432592	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17036960	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2888846	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34189496	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34346262	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35335704	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35519603	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7954485	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7954722	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7972183	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv510589	chr12:105670071-105743755	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs35325227	C12orf75	cis	Artery Aorta	GTEx
rs35325227	C12orf75	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105723800-105725200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr12:105723800-105725400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
3	chr12:105723800-105725400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr12:105723800-105725400	Active TSS	Brain Germinal Matrix	brain
5	chr12:105723800-105725600	Active TSS	Colonic Mucosa	Colon
6	chr12:105724000-105725000	Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr12:105724000-105725200	Active TSS	H9 Cell Line	embryonic stem cell
8	chr12:105724000-105725200	Active TSS	Esophagus	oesophagus
9	chr12:105724000-105725200	Active TSS	Ovary	ovary
10	chr12:105724000-105725400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:105724000-105725400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
12	chr12:105724000-105725400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr12:105724000-105725600	Active TSS	Placenta Amnion	Placenta Amnion
14	chr12:105724000-105725800	Active TSS	Fetal Kidney	kidney
15	chr12:105724000-105725800	Active TSS	Small Intestine	intestine
16	chr12:105724000-105726000	Active TSS	Pancreatic Islets	Pancreatic Islet
17	chr12:105724000-105726400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr12:105724200-105725000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
19	chr12:105724200-105725000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
20	chr12:105724200-105725000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr12:105724200-105725000	Active TSS	Primary hematopoietic stem cells	blood
22	chr12:105724200-105725000	Active TSS	Primary T helper naive cells fromperipheralblood	blood
23	chr12:105724200-105725000	Active TSS	Primary T helper cells fromperipheralblood	blood
24	chr12:105724200-105725000	Active TSS	Primary T regulatory cells fromperipheralblood	blood
25	chr12:105724200-105725000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr12:105724200-105725000	Active TSS	Cortex derived primary cultured neurospheres	brain
27	chr12:105724200-105725000	Active TSS	Colon Smooth Muscle	Colon
28	chr12:105724200-105725000	Active TSS	Duodenum Smooth Muscle	Duodenum
29	chr12:105724200-105725000	Active TSS	Psoas Muscle	Psoas
30	chr12:105724200-105725000	Active TSS	Rectal Mucosa Donor 29	rectum
31	chr12:105724200-105725000	Active TSS	HUVEC	blood vessel
32	chr12:105724200-105725200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr12:105724200-105725200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
34	chr12:105724200-105725200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
35	chr12:105724200-105725200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr12:105724200-105725200	Active TSS	Breast Myoepithelial Primary Cells	Breast
37	chr12:105724200-105725200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
38	chr12:105724200-105725200	Active TSS	Primary T helper naive cells from peripheral blood	blood
39	chr12:105724200-105725200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
40	chr12:105724200-105725200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr12:105724200-105725200	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
42	chr12:105724200-105725200	Active TSS	Brain Anterior Caudate	brain
43	chr12:105724200-105725200	Active TSS	Brain Cingulate Gyrus	brain
44	chr12:105724200-105725200	Active TSS	Brain Substantia Nigra	brain
45	chr12:105724200-105725200	Weak transcription	Fetal Heart	heart
46	chr12:105724200-105725200	Active TSS	Rectal Mucosa Donor 31	rectum
47	chr12:105724200-105725200	Active TSS	Hela-S3	cervix
48	chr12:105724200-105725400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr12:105724200-105725400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr12:105724200-105725400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell

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