Variant report

Variant	rs12405483
Chromosome Location	chr1:45211750-45211751
allele	A/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	POLR2A	chr1:45211747-45212433	K562	blood:	n/a	n/a
2	POLR2A	chr1:45211622-45211950	K562	blood:	n/a	n/a
3	POLR2A	chr1:45211540-45211801	HepG2	liver:	n/a	n/a
4	POLR2A	chr1:45211646-45211785	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:45210802..45212965-chr1:45265931..45268698,2	K562	blood:
2	chr1:45210546..45213904-chr1:45284220..45286382,3	K562	blood:
3	chr1:45211016..45213726-chr1:45240164..45242830,2	MCF-7	breast:

Variant related genes	Relation type
KIF2C	TF binding region
ENSG00000202444	Chromatin interaction
ENSG00000142937	Chromatin interaction
ENSG00000225721	Chromatin interaction
ENSG00000200913	Chromatin interaction
ENSG00000173846	Chromatin interaction
ENSG00000264294	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12405329	0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs17884321	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs17885777	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3795716	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs55898333	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56287310	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56413110	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58640576	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs59630460	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60022108	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs74070589	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs74070593	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74073404	0.96[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7524294	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][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	nsv533037	chr1:44361728-45333408	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
2	nsv998476	chr1:45001278-45311757	Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases
3	nsv534941	chr1:45001278-45311757	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases
4	nsv1014894	chr1:45139123-45397943	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	414 gene(s)	inside rSNPs	diseases
5	nsv529677	chr1:45179509-45748571	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	424 gene(s)	inside rSNPs	diseases
6	nsv1002026	chr1:45187594-45758048	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	386 gene(s)	inside rSNPs	diseases
7	nsv998871	chr1:45196587-45251179	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	171 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45205800-45240600	Weak transcription	Ovary	ovary
2	chr1:45206000-45223400	Weak transcription	Lung	lung
3	chr1:45206000-45240400	Weak transcription	Right Atrium	heart
4	chr1:45206200-45213400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr1:45206200-45218400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:45206200-45218800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr1:45206200-45220000	Weak transcription	Spleen	Spleen
8	chr1:45206200-45224800	Weak transcription	Esophagus	oesophagus
9	chr1:45206200-45225800	Weak transcription	Primary T cells from cord blood	blood
10	chr1:45206200-45227400	Weak transcription	Colonic Mucosa	Colon
11	chr1:45206200-45230200	Weak transcription	Rectal Smooth Muscle	rectum
12	chr1:45206200-45240400	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr1:45206200-45240600	Weak transcription	Stomach Mucosa	stomach
14	chr1:45206400-45211800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr1:45206400-45212000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr1:45206400-45213400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr1:45206400-45213400	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr1:45206400-45218400	Weak transcription	Gastric	stomach
19	chr1:45206400-45218400	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr1:45206400-45218600	Weak transcription	Primary B cells from peripheral blood	blood
21	chr1:45206400-45219000	Weak transcription	Primary B cells from cord blood	blood
22	chr1:45206400-45219600	Weak transcription	Placenta	Placenta
23	chr1:45206400-45221400	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr1:45206400-45232800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr1:45206400-45240600	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr1:45206600-45213000	Weak transcription	Primary hematopoietic stem cells	blood
27	chr1:45206600-45213400	Weak transcription	Fetal Brain Female	brain
28	chr1:45206600-45240600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr1:45206800-45211800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr1:45206800-45223000	Weak transcription	Fetal Kidney	kidney
31	chr1:45206800-45226600	Weak transcription	Fetal Brain Male	brain
32	chr1:45206800-45240200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr1:45207000-45211800	Weak transcription	Fetal Lung	lung
34	chr1:45207000-45216000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr1:45207000-45218800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr1:45207000-45233800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
37	chr1:45207200-45234200	Strong transcription	H1 Cell Line	embryonic stem cell
38	chr1:45207200-45234400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr1:45207400-45233800	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr1:45207600-45233800	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr1:45207600-45234400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr1:45208200-45212000	Strong transcription	Fetal Thymus	thymus
43	chr1:45208400-45214600	Strong transcription	NHEK	skin
44	chr1:45208400-45216600	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr1:45208600-45214400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
46	chr1:45208600-45233400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr1:45208600-45234000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr1:45208800-45213400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr1:45208800-45234400	Strong transcription	HUES6 Cell Line	embryonic stem cell
50	chr1:45209000-45212000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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