Variant report

Variant	rs12264657
Chromosome Location	chr10:52833902-52833903
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	POLR2A	chr10:52833776-52834795	ProgFib	skin:	n/a	n/a
2	RAD21	chr10:52833441-52834820	SK-N-SH_RA	brain:	n/a	chr10:52834326-52834339 chr10:52833797-52833810 chr10:52834336-52834349
3	E2F6	chr10:52833015-52834957	H1-hESC	embryonic stem cell:	n/a	chr10:52833251-52833259 chr10:52834020-52834029 chr10:52833249-52833260 chr10:52833252-52833259 chr10:52833250-52833260 chr10:52834684-52834699 chr10:52833251-52833259 chr10:52834034-52834043
4	TAF1	chr10:52833359-52834761	H1-hESC	embryonic stem cell:	n/a	n/a
5	MXI1	chr10:52833256-52835376	SK-N-SH	brain:	n/a	n/a
6	CTCF	chr10:52833800-52833950	BJ	skin:	n/a	n/a
7	MAX	chr10:52833408-52834997	H1-hESC	embryonic stem cell:	n/a	n/a
8	MXI1	chr10:52833222-52835153	IMR90	lung:	n/a	n/a
9	SIN3A	chr10:52833212-52835382	H1-hESC	embryonic stem cell:	n/a	n/a
10	MAX	chr10:52833487-52834917	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr10:52833167-52834860	H1-hESC	embryonic stem cell:	n/a	n/a
12	RAD21	chr10:52833824-52834789	H1-hESC	embryonic stem cell:	n/a	chr10:52834326-52834339 chr10:52834336-52834349
13	POLR2A	chr10:52833560-52834743	IMR90	lung:	n/a	n/a
14	POLR2A	chr10:52833900-52834545	SK-N-SH	brain:	n/a	n/a
15	POLR2A	chr10:52833822-52834639	U87	brain:	n/a	n/a
16	ZNF263	chr10:52832847-52835072	HEK293-T-REx	kidney:	n/a	chr10:52834013-52834022 chr10:52834309-52834330 chr10:52834289-52834298
17	CTBP2	chr10:52833262-52834832	H1-hESC	embryonic stem cell:	n/a	n/a
18	TBP	chr10:52833286-52834782	H1-hESC	embryonic stem cell:	n/a	n/a
19	MAX	chr10:52833530-52834931	SK-N-SH	brain:	n/a	n/a
20	POLR2A	chr10:52833819-52834845	H1-neurons	neurons:	n/a	n/a
21	POLR2A	chr10:52833816-52834645	U87	brain:	n/a	n/a
22	RAD21	chr10:52833404-52834709	H1-hESC	embryonic stem cell:	n/a	chr10:52834326-52834339 chr10:52833797-52833810 chr10:52834336-52834349
23	POLR2A	chr10:52833410-52834870	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr10:52833327-52834655	Gliobla	brain:	n/a	n/a
25	TEAD4	chr10:52833440-52833953	H1-hESC	embryonic stem cell:	n/a	n/a
26	NRF1	chr10:52833353-52834743	SK-N-SH	brain:	n/a	chr10:52833541-52833550 chr10:52834191-52834205
27	E2F6	chr10:52833414-52834895	H1-hESC	embryonic stem cell:	n/a	chr10:52834020-52834029 chr10:52834684-52834699 chr10:52834034-52834043
28	RAD21	chr10:52833206-52834919	IMR90	lung:	n/a	chr10:52834326-52834339 chr10:52833797-52833810 chr10:52834336-52834349
29	BACH1	chr10:52833419-52834110	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr10:52833460-52834542	HEK293	kidney:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr10:52833902-52833952	NB4	blood:	n/a
2	chr10:52833902-52833952	MCF-7	breast:	n/a
3	chr10:52833902-52833952	NHBE	bronchial:	n/a
4	chr10:52833902-52833952	GM06990	blood:	n/a
5	chr10:52833902-52833952	SK-N-SH	brain:	n/a
6	chr10:52833902-52833952	BJ	skin:	n/a
7	chr10:52833902-52833952	SAEC	small airway:	n/a
8	chr10:52833902-52833952	HRE	kidney:	n/a
9	chr10:52833902-52833952	AG04450	lung:	fetal
10	chr10:52833902-52833952	SK-N-MC	brain:	n/a
11	chr10:52833902-52833952	K562	blood:	n/a
12	chr10:52833902-52833952	Caco-2	colon:	n/a
13	chr10:52833902-52833952	GM12878	blood:	n/a
14	chr10:52833902-52833952	U87	brain:	n/a
15	chr10:52833902-52833952	HMEC	breast:	n/a
16	chr10:52833902-52833952	HEK293	kidney:	embryo
17	chr10:52833902-52833952	GM12891	blood:	n/a
18	chr10:52833902-52833952	HCT-116	colon:	n/a
19	chr10:52833902-52833952	GM19239	blood:	n/a
20	chr10:52833902-52833952	Hela-S3	cervix:	n/a
21	chr10:52833902-52833952	GM12892	blood:	n/a
22	chr10:52833902-52833952	AoSMC	blood vessel:	n/a
23	chr10:52833902-52833952	CMK	blood:	n/a
24	chr10:52833902-52833952	HAEpiC	amniotic membrane:	n/a
25	chr10:52833902-52833952	NHDF-neo	bronchial:	n/a
26	chr10:52833902-52833952	Hepatocyte	liver:	n/a
27	chr10:52833902-52833952	HCPEpiC	choroid plexus:	n/a
28	chr10:52833902-52833952	HRCEpiC	kidney:	n/a
29	chr10:52833902-52833952	AG04449	skin:	fetal
30	chr10:52833902-52833952	PANC-1	pancreas:	n/a
31	chr10:52833902-52833952	HepG2	liver:	n/a
32	chr10:52833902-52833952	MCF10A-Er-Src	breast:	n/a
33	chr10:52833902-52833952	NH-A	brain:	n/a
34	chr10:52833902-52833952	AG10803	skin:	n/a
35	chr10:52833902-52833952	HCF	heart:	n/a
36	chr10:52833902-52833952	HEEpiC	esophagus:	n/a
37	chr10:52833902-52833952	HCM	heart:	n/a
38	chr10:52833902-52833952	SK-N-SH_RA	brain:	n/a
39	chr10:52833902-52833952	NT2-D1	testis:	n/a
40	chr10:52833902-52833952	HIPEpiC	eye:	n/a
41	chr10:52833902-52833952	BE2_C	brain:	n/a
42	chr10:52833902-52833952	RPTEC	kidney:	n/a
43	chr10:52833902-52833952	SKMC	muscle:	n/a
44	chr10:52833902-52833952	Jurkat	blood:	n/a
45	chr10:52833902-52833952	LNCaP	prostate:	n/a
46	chr10:52833902-52833952	ovcar-3	ovarian:	n/a
47	chr10:52833902-52833952	HRPEpiC	eye:	n/a
48	chr10:52833902-52833952	PrEC	prostate:	n/a
49	chr10:52833902-52833952	PFSK-1	brain:	n/a
50	chr10:52833902-52833952	ECC-1	luminal epithelium:	n/a

Variant related genes	Relation type
PRKG1	TF binding region
PRKG1	CpG island

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10218997	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10995567	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10995590	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11813092	1.00[CEU][hapmap]
rs12247631	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12253781	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12265235	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2339626	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2339670	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2660210	1.00[CEU][hapmap]
rs28438967	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2879545	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs5011544	1.00[MEX][hapmap]
rs7096841	1.00[CEU][hapmap]
rs74133958	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7476747	1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831873	chr10:52710610-52899540	Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv895394	chr10:52793177-52866503	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1036645	chr10:52804961-53159076	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52832800-52834200	Enhancers	Fetal Brain Male	brain
2	chr10:52832800-52834400	Active TSS	H1 Cell Line	embryonic stem cell
3	chr10:52832800-52835400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
4	chr10:52832800-52837400	Active TSS	Breast Myoepithelial Primary Cells	Breast
5	chr10:52832800-52840000	Active TSS	Aorta	Aorta
6	chr10:52833000-52834200	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
7	chr10:52833000-52834400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr10:52833000-52834400	Active TSS	Brain Cingulate Gyrus	brain
9	chr10:52833000-52834400	Active TSS	Skeletal Muscle Female	skeletal muscle
10	chr10:52833000-52834600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr10:52833000-52834800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr10:52833000-52835000	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
13	chr10:52833000-52835200	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
14	chr10:52833000-52835800	Active TSS	Fetal Kidney	kidney
15	chr10:52833000-52836200	Active TSS	Psoas Muscle	Psoas
16	chr10:52833000-52836400	Active TSS	Right Ventricle	heart
17	chr10:52833000-52837000	Active TSS	Right Atrium	heart
18	chr10:52833000-52837600	Active TSS	Colon Smooth Muscle	Colon
19	chr10:52833200-52834200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
20	chr10:52833200-52834400	Active TSS	HSMM	muscle
21	chr10:52833200-52834400	Bivalent/Poised TSS	NHEK	skin
22	chr10:52833200-52834600	Active TSS	iPS-20b Cell Line	embryonic stem cell
23	chr10:52833200-52834600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
24	chr10:52833200-52834600	Active TSS	Muscle Satellite Cultured Cells	--
25	chr10:52833200-52834800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr10:52833200-52834800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr10:52833200-52834800	Active TSS	iPS-15b Cell Line	embryonic stem cell
28	chr10:52833200-52834800	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
29	chr10:52833200-52834800	Bivalent/Poised TSS	Thymus	Thymus
30	chr10:52833200-52834800	Bivalent/Poised TSS	A549	lung
31	chr10:52833200-52834800	Active TSS	NH-A	brain
32	chr10:52833200-52835000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr10:52833200-52835000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr10:52833200-52835000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
35	chr10:52833200-52835000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
36	chr10:52833200-52835000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr10:52833200-52835000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr10:52833200-52835000	Active TSS	Esophagus	oesophagus
39	chr10:52833200-52835000	Flanking Active TSS	Placenta	Placenta
40	chr10:52833200-52835200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr10:52833200-52835200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
42	chr10:52833200-52835200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
43	chr10:52833200-52835200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr10:52833200-52835200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
45	chr10:52833200-52835400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr10:52833200-52835400	Active TSS	NHDF-Ad	bronchial
47	chr10:52833200-52835600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr10:52833200-52835600	Active TSS	Colonic Mucosa	Colon
49	chr10:52833200-52835600	Active TSS	Left Ventricle	heart
50	chr10:52833200-52835800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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