Variant report

Variant	rs12564199
Chromosome Location	chr1:153948540-153948541
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:153948322-153948640	GM12878	blood:	n/a	n/a
2	POLR2A	chr1:153948202-153948769	K562	blood:	n/a	n/a
3	POLR2A	chr1:153948258-153948742	MCF-7	breast:	n/a	n/a
4	POLR2A	chr1:153948436-153948581	K562	blood:	n/a	n/a
5	POLR2A	chr1:153948016-153948743	SK-N-MC	brain:	n/a	n/a
6	POLR2A	chr1:153948200-153948663	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr1:153948396-153951468	HepG2	liver:	n/a	n/a
8	POLR2A	chr1:153948080-153948667	PFSK-1	brain:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:153948305..153949945-chr17:41176820..41178992,2	MCF-7	breast:
2	chr1:153892664..153896587-chr1:153948190..153951187,6	K562	blood:
3	chr1:153901414..153903833-chr1:153945059..153949290,4	K562	blood:
4	chr1:153645392..153647904-chr1:153946956..153949056,3	K562	blood:
5	chr1:153915931..153921352-chr1:153944041..153951714,10	K562	blood:
6	chr1:153948325..153950818-chr1:154153014..154155918,2	MCF-7	breast:
7	chr1:153947481..153949657-chr15:50646074..50648130,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000272654	TF binding region
ENSG00000108828	Chromatin interaction
ENSG00000143614	Chromatin interaction
ENSG00000108830	Chromatin interaction
ENSG00000198837	Chromatin interaction
ENSG00000244879	Chromatin interaction
ENSG00000104064	Chromatin interaction
ENSG00000143549	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12563539	0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2066134	1.00[CEU][hapmap];0.94[JPT][hapmap]
rs2841102	0.83[JPT][hapmap]
rs4845584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4845591	0.94[JPT][hapmap]
rs4845593	0.94[JPT][hapmap]
rs60382526	0.97[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6666957	0.83[AMR][1000 genomes]
rs6676863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs73010774	0.96[EUR][1000 genomes]
rs7415816	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	nsv531892	chr1:153671910-153954090	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
4	nsv532551	chr1:153732039-154192279	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
5	esv1830240	chr1:153885261-154370938	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	239 gene(s)	inside rSNPs	diseases
6	nsv532552	chr1:153912047-153950752	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153941200-153948600	Weak transcription	Psoas Muscle	Psoas
2	chr1:153941200-153949000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:153941400-153949800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:153941600-153948800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr1:153944600-153948600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr1:153944600-153948600	Strong transcription	Fetal Muscle Trunk	muscle
7	chr1:153945000-153948600	Strong transcription	Brain Hippocampus Middle	brain
8	chr1:153945000-153948600	Strong transcription	Fetal Stomach	stomach
9	chr1:153945400-153948600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr1:153945400-153948600	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr1:153945400-153948600	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr1:153945600-153948600	Strong transcription	H9 Cell Line	embryonic stem cell
13	chr1:153945600-153948600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
14	chr1:153945600-153948600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr1:153945800-153948600	Strong transcription	Ovary	ovary
16	chr1:153946000-153949000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr1:153946400-153948600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:153946600-153948800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr1:153946800-153949000	Weak transcription	Small Intestine	intestine
20	chr1:153947000-153948800	Genic enhancers	Monocytes-CD14+_RO01746	blood
21	chr1:153947200-153948800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr1:153947400-153948800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr1:153947400-153949200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr1:153947400-153949200	Weak transcription	Aorta	Aorta
25	chr1:153947400-153949200	Weak transcription	Esophagus	oesophagus
26	chr1:153948000-153949000	Genic enhancers	Primary T cells fromperipheralblood	blood
27	chr1:153948000-153949200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr1:153948200-153948600	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr1:153948200-153948600	Transcr. at gene 5' and 3'	Primary T cells from cord blood	blood
30	chr1:153948200-153948600	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr1:153948200-153948600	Transcr. at gene 5' and 3'	Duodenum Mucosa	Duodenum
32	chr1:153948200-153948600	Genic enhancers	Fetal Intestine Small	intestine
33	chr1:153948200-153948600	Genic enhancers	Pancreas	Pancrea
34	chr1:153948200-153948600	Genic enhancers	Rectal Mucosa Donor 31	rectum
35	chr1:153948200-153948600	Genic enhancers	Sigmoid Colon	Sigmoid Colon
36	chr1:153948200-153948600	Genic enhancers	Spleen	Spleen
37	chr1:153948200-153948600	Genic enhancers	HepG2	liver
38	chr1:153948200-153948600	Genic enhancers	Osteobl	bone
39	chr1:153948200-153948800	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
40	chr1:153948200-153948800	Genic enhancers	Primary hematopoietic stem cells	blood
41	chr1:153948200-153948800	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr1:153948200-153948800	Enhancers	Primary T helper naive cells from peripheral blood	blood
43	chr1:153948200-153948800	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
44	chr1:153948200-153948800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
45	chr1:153948200-153948800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
46	chr1:153948200-153948800	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
47	chr1:153948200-153948800	Genic enhancers	Muscle Satellite Cultured Cells	--
48	chr1:153948200-153948800	Genic enhancers	Adipose Nuclei	Adipose
49	chr1:153948200-153948800	Genic enhancers	Liver	Liver
50	chr1:153948200-153948800	Genic enhancers	Duodenum Smooth Muscle	Duodenum

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