Variant report

Variant	rs73281085
Chromosome Location	chr12:45270700-45270701
allele	C/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	ZNF143	chr12:45270119-45270966	H1-hESC	embryonic stem cell:	n/a	n/a
2	CTCF	chr12:45270560-45270710	GM12871	blood:	n/a	chr12:45270691-45270704
3	REST	chr12:45270451-45271013	GM12878	blood:	n/a	chr12:45270531-45270544 chr12:45270779-45270788
4	SIN3AK20	chr12:45270175-45270890	H1-hESC	embryonic stem cell:	n/a	n/a
5	REST	chr12:45270485-45270881	PANC-1	pancreas:	n/a	chr12:45270531-45270544 chr12:45270779-45270788
6	CTCF	chr12:45270465-45270869	MCF-7	breast:	n/a	chr12:45270691-45270704
7	CTCF	chr12:45270580-45270730	RPTEC	kidney:	n/a	chr12:45270691-45270704
8	SRF	chr12:45270160-45271090	ECC-1	luminal epithelium:	n/a	chr12:45270193-45270203
9	REST	chr12:45270565-45271013	SK-N-SH	brain:	n/a	chr12:45270779-45270788
10	CTCF	chr12:45270620-45270770	AG09309	skin:	n/a	chr12:45270691-45270704
11	REST	chr12:45270549-45270899	PANC-1	pancreas:	n/a	chr12:45270779-45270788
12	MAX	chr12:45270100-45270900	A549	lung:	n/a	n/a
13	REST	chr12:45270134-45271334	ECC-1	luminal epithelium:	n/a	chr12:45270531-45270544 chr12:45270779-45270788 chr12:45270351-45270365
14	POLR2A	chr12:45270674-45270721	H1-hESC	embryonic stem cell:	n/a	n/a
15	REST	chr12:45270568-45270934	SK-N-SH	brain:	n/a	chr12:45270779-45270788
16	REST	chr12:45270655-45270836	HepG2	liver:	n/a	chr12:45270779-45270788
17	REST	chr12:45270217-45271159	A549	lung:	n/a	chr12:45270531-45270544 chr12:45270779-45270788 chr12:45270351-45270365
18	CTCF	chr12:45270483-45270851	MCF-7	breast:	n/a	chr12:45270691-45270704
19	RAD21	chr12:45270337-45271020	H1-hESC	embryonic stem cell:	n/a	chr12:45270798-45270808 chr12:45270534-45270547 chr12:45270766-45270780
20	CTCF	chr12:45270511-45270919	H1-hESC	embryonic stem cell:	n/a	chr12:45270691-45270704
21	TAF1	chr12:45268863-45270739	H1-hESC	embryonic stem cell:	n/a	n/a
22	CTCF	chr12:45270580-45270730	HPF	lung:	n/a	chr12:45270691-45270704
23	CTCF	chr12:45270560-45270710	AG09319	gingival:	n/a	chr12:45270691-45270704
24	REST	chr12:45270532-45271027	HL-60	blood:	n/a	chr12:45270779-45270788
25	REST	chr12:45270152-45271156	MCF-7	breast:	n/a	chr12:45270531-45270544 chr12:45270779-45270788 chr12:45270351-45270365
26	CTCF	chr12:45270560-45270710	HUVEC	blood vessel:	n/a	chr12:45270691-45270704
27	REST	chr12:45270472-45271139	HL-60	blood:	n/a	chr12:45270531-45270544 chr12:45270779-45270788
28	REST	chr12:45270086-45271156	PFSK-1	brain:	n/a	chr12:45270531-45270544 chr12:45270779-45270788 chr12:45270351-45270365
29	ZBTB7A	chr12:45269031-45271159	ECC-1	luminal epithelium:	n/a	chr12:45270797-45270806 chr12:45269905-45269913
30	E2F6	chr12:45270122-45270748	A549	lung:	n/a	n/a
31	SIN3AK20	chr12:45270638-45270851	PFSK-1	brain:	n/a	n/a
32	REST	chr12:45270309-45271229	MCF-7	breast:	n/a	chr12:45270531-45270544 chr12:45270779-45270788 chr12:45270351-45270365
33	ZBTB7A	chr12:45268901-45271105	ECC-1	luminal epithelium:	n/a	chr12:45270797-45270806 chr12:45269905-45269913
34	POLR2A	chr12:45269560-45270774	H1-neurons	neurons:	n/a	n/a
35	CTCF	chr12:45270600-45270750	A549	lung:	n/a	chr12:45270691-45270704
36	CTCF	chr12:45270580-45270730	HCM	heart:	n/a	chr12:45270691-45270704
37	REST	chr12:45270565-45270896	GM12878	blood:	n/a	chr12:45270779-45270788
38	CTBP2	chr12:45270203-45270964	H1-hESC	embryonic stem cell:	n/a	n/a
39	MAX	chr12:45270055-45271045	H1-hESC	embryonic stem cell:	n/a	n/a
40	MXI1	chr12:45268594-45271198	SK-N-SH	brain:	n/a	n/a
41	REST	chr12:45270651-45270842	U87	brain:	n/a	chr12:45270779-45270788
42	SRF	chr12:45270232-45271096	ECC-1	luminal epithelium:	n/a	n/a
43	TCF12	chr12:45269830-45271017	ECC-1	luminal epithelium:	n/a	n/a
44	CTCF	chr12:45270451-45270831	MCF-7	breast:	n/a	chr12:45270691-45270704
45	MAX	chr12:45270099-45270972	MCF-7	breast:	n/a	n/a
46	REST	chr12:45269036-45271162	H1-neurons	neurons:	n/a	chr12:45270531-45270544 chr12:45270779-45270788 chr12:45270351-45270365
47	REST	chr12:45270594-45270934	PANC-1	pancreas:	n/a	chr12:45270779-45270788
48	CTCF	chr12:45270660-45270810	Caco-2	colon:	n/a	chr12:45270691-45270704
49	ZBTB7A	chr12:45270658-45270894	K562	blood:	n/a	chr12:45270797-45270806
50	REST	chr12:45270505-45271039	U87	brain:	n/a	chr12:45270531-45270544 chr12:45270779-45270788

Variant related genes	Relation type
NELL2	TF binding region

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs2703058	1.00[AMR][1000 genomes]
rs2710422	1.00[AMR][1000 genomes]
rs2710423	1.00[AMR][1000 genomes]
rs369442	1.00[AMR][1000 genomes]
rs60628417	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73277302	1.00[AMR][1000 genomes]
rs73279103	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73279110	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73279111	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73279124	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73279126	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73279129	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73279149	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73279151	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73279187	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73283041	1.00[AMR][1000 genomes]
rs73283042	1.00[AMR][1000 genomes]
rs73284986	1.00[AMR][1000 genomes]
rs73287008	1.00[AMR][1000 genomes]
rs73287009	1.00[AMR][1000 genomes]
rs73288937	1.00[AMR][1000 genomes]
rs73288940	1.00[AMR][1000 genomes]
rs73288992	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1036926	chr12:45131884-45273648	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
2	nsv541484	chr12:45131884-45273648	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:45264800-45271200	Active TSS	Fetal Brain Male	brain
2	chr12:45266800-45270800	Active TSS	Primary T killer memory cells from peripheral blood	blood
3	chr12:45267200-45271000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:45267200-45271400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr12:45267800-45271000	Bivalent/Poised TSS	Primary T cells from cord blood	blood
6	chr12:45268000-45270800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:45268000-45270800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr12:45268000-45271000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
9	chr12:45268000-45271200	Active TSS	H9 Cell Line	embryonic stem cell
10	chr12:45268200-45271200	Active TSS	H1 Cell Line	embryonic stem cell
11	chr12:45268600-45271000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr12:45268600-45271200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
13	chr12:45268800-45270800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
14	chr12:45268800-45270800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr12:45268800-45271000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr12:45268800-45271000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
17	chr12:45268800-45271200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr12:45268800-45271200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr12:45268800-45271200	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr12:45269000-45270800	Bivalent/Poised TSS	Fetal Intestine Small	intestine
21	chr12:45269000-45271000	Active TSS	HUES48 Cell Line	embryonic stem cell
22	chr12:45269000-45271000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr12:45269000-45271000	Active TSS	Aorta	Aorta
24	chr12:45269000-45271000	Active TSS	Brain Angular Gyrus	brain
25	chr12:45269200-45270800	Active TSS	HUES64 Cell Line	embryonic stem cell
26	chr12:45269200-45270800	Bivalent/Poised TSS	Fetal Intestine Large	intestine
27	chr12:45269200-45270800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
28	chr12:45269200-45271000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
29	chr12:45269200-45271000	Active TSS	iPS-15b Cell Line	embryonic stem cell
30	chr12:45269200-45271000	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
31	chr12:45269200-45271000	Bivalent/Poised TSS	HSMMtube	muscle
32	chr12:45269400-45270800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr12:45269400-45270800	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr12:45269400-45270800	Bivalent/Poised TSS	HSMM	muscle
35	chr12:45269400-45271000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr12:45269400-45271200	Active TSS	Fetal Kidney	kidney
37	chr12:45269400-45271400	Active TSS	iPS-18 Cell Line	embryonic stem cell
38	chr12:45269600-45270800	Active TSS	Primary T helper naive cells from peripheral blood	blood
39	chr12:45269600-45270800	Flanking Active TSS	Colonic Mucosa	Colon
40	chr12:45269600-45270800	Active TSS	Colon Smooth Muscle	Colon
41	chr12:45269600-45270800	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
42	chr12:45269600-45270800	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
43	chr12:45269600-45270800	Active TSS	K562	blood
44	chr12:45269600-45271000	Active TSS	iPS-20b Cell Line	embryonic stem cell
45	chr12:45269600-45271000	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr12:45269600-45271000	Active TSS	Brain Substantia Nigra	brain
47	chr12:45269600-45271200	Active TSS	Brain Anterior Caudate	brain
48	chr12:45269600-45271200	Active TSS	Brain Inferior Temporal Lobe	brain
49	chr12:45269800-45270800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr12:45269800-45270800	Bivalent/Poised TSS	NHLF	lung

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