Variant report

Variant	rs12406301
Chromosome Location	chr1:211306786-211306787
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	E2F6	chr1:211306355-211307864	H1-hESC	embryonic stem cell:	n/a	chr1:211307459-211307470 chr1:211307544-211307554
2	CTCF	chr1:211306637-211308259	A549	lung:	n/a	chr1:211307425-211307438 chr1:211307562-211307575 chr1:211307560-211307578 chr1:211307673-211307686 chr1:211307518-211307531 chr1:211307561-211307577 chr1:211307562-211307575
3	MAX	chr1:211306455-211307651	H1-hESC	embryonic stem cell:	n/a	chr1:211306746-211306756
4	MAZ	chr1:211306729-211307789	IMR90	lung:	n/a	chr1:211306746-211306756
5	RAD21	chr1:211305554-211309271	SK-N-SH	brain:	n/a	chr1:211307669-211307688 chr1:211308869-211308888 chr1:211307118-211307132 chr1:211308209-211308219 chr1:211307422-211307436 chr1:211307673-211307687 chr1:211307586-211307599 chr1:211307558-211307577 chr1:211308879-211308886
6	CTCF	chr1:211306699-211309685	SK-N-SH	brain:	n/a	chr1:211308873-211308886 chr1:211307425-211307438 chr1:211308872-211308888 chr1:211307562-211307575 chr1:211307560-211307578 chr1:211307673-211307686 chr1:211307518-211307531 chr1:211307561-211307577 chr1:211307562-211307575
7	E2F6	chr1:211306492-211307077	H1-hESC	embryonic stem cell:	n/a	n/a
8	HMGN3	chr1:211306686-211306906	K562	blood:	n/a	n/a
9	SMC3	chr1:211306536-211309262	SK-N-SH	brain:	n/a	chr1:211307562-211307576 chr1:211307118-211307132
10	MAX	chr1:211306586-211307904	A549	lung:	n/a	chr1:211307794-211307803 chr1:211306746-211306756
11	MAX	chr1:211306506-211307969	A549	lung:	n/a	chr1:211307794-211307803 chr1:211306746-211306756
12	POLR2A	chr1:211306652-211307788	H1-neurons	neurons:	n/a	n/a
13	MAX	chr1:211306426-211307115	H1-hESC	embryonic stem cell:	n/a	chr1:211306746-211306756
14	GATA2	chr1:211306573-211308155	SH-SY5Y	brain:	n/a	chr1:211306947-211306956 chr1:211306949-211306956 chr1:211306942-211306963 chr1:211306947-211306957 chr1:211306949-211306956 chr1:211306949-211306956
15	POLR2A	chr1:211306597-211307112	H1-neurons	neurons:	n/a	n/a
16	E2F6	chr1:211306766-211307790	A549	lung:	n/a	chr1:211307459-211307470 chr1:211307544-211307554
17	REST	chr1:211306450-211307945	H1-neurons	neurons:	n/a	chr1:211307068-211307081 chr1:211307532-211307545 chr1:211307661-211307674
18	CTCF	chr1:211306780-211306930	BJ	skin:	n/a	n/a
19	POLR2A	chr1:211306699-211307743	Gliobla	brain:	n/a	n/a
20	CTBP2	chr1:211306663-211307807	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
KCNH1-IT1	TF binding region

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10863877	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11119694	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11119696	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11579711	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12408290	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1338353	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1538287	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1582137	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17017226	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17188895	0.93[ASN][1000 genomes]
rs1933524	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2211039	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28826269	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3111218	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3111220	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3111221	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3111224	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3111226	0.82[AFR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3120775	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3120776	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3120777	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3120778	0.84[AFR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3125850	0.84[AFR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3125852	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3811396	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3828021	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61848604	0.93[ASN][1000 genomes]
rs61848648	0.84[ASN][1000 genomes]
rs6540658	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6540659	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6540666	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6540667	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6540669	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6669706	0.95[ASN][1000 genomes]
rs6684075	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6700303	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7516636	0.93[ASN][1000 genomes]
rs7530182	0.84[AFR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs867849	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9430056	0.84[AFR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9430057	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9430058	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:211302600-211307800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
2	chr1:211303800-211307800	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr1:211304000-211307600	Active TSS	Brain Angular Gyrus	brain
4	chr1:211305200-211307600	Active TSS	Brain Anterior Caudate	brain
5	chr1:211305200-211307800	Active TSS	HSMMtube	muscle
6	chr1:211305400-211307800	Active TSS	HSMM	muscle
7	chr1:211306000-211306800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr1:211306000-211306800	Flanking Active TSS	Brain Hippocampus Middle	brain
9	chr1:211306000-211307200	Bivalent/Poised TSS	Colonic Mucosa	Colon
10	chr1:211306000-211307400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
11	chr1:211306000-211307600	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr1:211306000-211308000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr1:211306200-211306800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr1:211306200-211306800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
15	chr1:211306200-211306800	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
16	chr1:211306200-211306800	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
17	chr1:211306200-211306800	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
18	chr1:211306200-211306800	Flanking Bivalent TSS/Enh	Osteobl	bone
19	chr1:211306200-211307000	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
20	chr1:211306200-211307000	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
21	chr1:211306200-211307400	Bivalent/Poised TSS	NHDF-Ad	bronchial
22	chr1:211306200-211307800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr1:211306200-211307800	Active TSS	Brain Substantia Nigra	brain
24	chr1:211306400-211306800	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr1:211306400-211306800	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr1:211306400-211306800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr1:211306400-211306800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
28	chr1:211306400-211306800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr1:211306400-211306800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
30	chr1:211306400-211306800	Bivalent Enhancer	Liver	Liver
31	chr1:211306400-211306800	Flanking Active TSS	Colon Smooth Muscle	Colon
32	chr1:211306400-211306800	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
33	chr1:211306400-211306800	Flanking Bivalent TSS/Enh	Fetal Brain Male	brain
34	chr1:211306400-211306800	Flanking Bivalent TSS/Enh	NH-A	brain
35	chr1:211306400-211307000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
36	chr1:211306400-211307000	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
37	chr1:211306400-211307000	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
38	chr1:211306400-211307000	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr1:211306400-211307200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr1:211306400-211307200	Bivalent/Poised TSS	Psoas Muscle	Psoas
41	chr1:211306400-211307400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr1:211306400-211307400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
43	chr1:211306400-211307400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
44	chr1:211306400-211307400	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
45	chr1:211306400-211307400	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
46	chr1:211306400-211307600	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr1:211306400-211307600	Bivalent/Poised TSS	Fetal Brain Female	brain
48	chr1:211306400-211307800	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
49	chr1:211306400-211308000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
50	chr1:211306600-211306800	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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