Variant report

Variant	rs3219473
Chromosome Location	chr1:45803946-45803947
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:22)
CpG islands
(count:61)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:22 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:45803692-45804394	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr1:45803626-45804105	K562	blood:	n/a	n/a
3	POLR2A	chr1:45803814-45804186	HepG2	liver:	n/a	n/a
4	POLR2A	chr1:45803420-45804401	HepG2	liver:	n/a	n/a
5	POLR2A	chr1:45803509-45804284	HepG2	liver:	n/a	n/a
6	POLR2A	chr1:45803840-45804099	MCF-7	breast:	n/a	n/a
7	POLR2A	chr1:45803930-45804335	GM12878	blood:	n/a	n/a
8	POLR2A	chr1:45803822-45804367	U87	brain:	n/a	n/a
9	HEY1	chr1:45803789-45804378	HepG2	liver:	n/a	n/a
10	POLR2A	chr1:45803622-45804121	K562	blood:	n/a	n/a
11	POLR2A	chr1:45803842-45804078	HCT-116	colon:	n/a	n/a
12	POLR2A	chr1:45803734-45804043	SK-N-SH	brain:	n/a	n/a
13	POLR2A	chr1:45803635-45804084	K562	blood:	n/a	n/a
14	POLR2A	chr1:45803756-45804299	GM12892	blood:	n/a	n/a
15	POLR2A	chr1:45803620-45804096	PFSK-1	brain:	n/a	n/a
16	POLR2A	chr1:45803225-45804518	K562	blood:	n/a	n/a
17	POLR2A	chr1:45803810-45804049	HUVEC	blood vessel:	n/a	n/a
18	POLR2A	chr1:45803932-45803947	MCF-7	breast:	n/a	n/a
19	POLR2A	chr1:45803563-45804552	PFSK-1	brain:	n/a	n/a
20	POLR2A	chr1:45803638-45804203	GM12878	blood:	n/a	n/a
21	POLR2A	chr1:45803830-45804056	H1-hESC	embryonic stem cell:	n/a	n/a
22	PAX5	chr1:45803812-45804047	GM12878	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:45803944-45803994	HCM	heart:	n/a
2	chr1:45803944-45803994	AG04449	skin:	fetal
3	chr1:45803944-45803994	Hepatocyte	liver:	n/a
4	chr1:45803944-45803994	SK-N-MC	brain:	n/a
5	chr1:45803944-45803994	NHDF-neo	bronchial:	n/a
6	chr1:45803944-45803994	AG09309	skin:	n/a
7	chr1:45803944-45803994	HCT-116	colon:	n/a
8	chr1:45803944-45803994	HPAEpiC	pulmonary alveolar:	n/a
9	chr1:45803944-45803994	K562	blood:	n/a
10	chr1:45803944-45803994	AG10803	skin:	n/a
11	chr1:45803944-45803994	ProgFib	skin:	n/a
12	chr1:45803944-45803994	SK-N-SH	brain:	n/a
13	chr1:45803944-45803994	GM19239	blood:	n/a
14	chr1:45803944-45803994	Jurkat	blood:	n/a
15	chr1:45803944-45803994	RPTEC	kidney:	n/a
16	chr1:45803944-45803994	AG04450	lung:	fetal
17	chr1:45803944-45803994	GM12878	blood:	n/a
18	chr1:45803944-45803994	U87	brain:	n/a
19	chr1:45803944-45803994	HIPEpiC	eye:	n/a
20	chr1:45803944-45803994	Hela-S3	cervix:	n/a
21	chr1:45803944-45803994	NH-A	brain:	n/a
22	chr1:45803944-45803994	HMEC	breast:	n/a
23	chr1:45803944-45803994	NHBE	bronchial:	n/a
24	chr1:45803944-45803994	HCPEpiC	choroid plexus:	n/a
25	chr1:45803944-45803994	ECC-1	luminal epithelium:	n/a
26	chr1:45803944-45803994	IMR90	lung:	fetal
27	chr1:45803944-45803994	SKMC	muscle:	n/a
28	chr1:45803944-45803994	NT2-D1	testis:	n/a
29	chr1:45803944-45803994	GM12891	blood:	n/a
30	chr1:45803944-45803994	H1-hESC	embryonic stem cell:	embryo
31	chr1:45803944-45803994	HNPCEpiC	eye:	n/a
32	chr1:45803944-45803994	SAEC	small airway:	n/a
33	chr1:45803944-45803994	SK-N-SH_RA	brain:	n/a
34	chr1:45803944-45803994	MCF-7	breast:	n/a
35	chr1:45803944-45803994	PrEC	prostate:	n/a
36	chr1:45803944-45803994	BJ	skin:	n/a
37	chr1:45803944-45803994	GM06990	blood:	n/a
38	chr1:45803944-45803994	BE2_C	brain:	n/a
39	chr1:45803944-45803994	Caco-2	colon:	n/a
40	chr1:45803944-45803994	HL-60	blood:	n/a
41	chr1:45803944-45803994	PANC-1	pancreas:	n/a
42	chr1:45803944-45803994	HRE	kidney:	n/a
43	chr1:45803944-45803994	HRPEpiC	eye:	n/a
44	chr1:45803944-45803994	AG09319	gingival:	n/a
45	chr1:45803944-45803994	ovcar-3	ovarian:	n/a
46	chr1:45803944-45803994	CMK	blood:	n/a
47	chr1:45803944-45803994	NB4	blood:	n/a
48	chr1:45803944-45803994	HEK293	kidney:	embryo
49	chr1:45803944-45803994	MCF10A-Er-Src	breast:	n/a
50	chr1:45803944-45803994	HCF	heart:	n/a

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:45282552..45287322-chr1:45800975..45809178,15	K562	blood:
2	chr1:45803780..45809046-chr1:46047811..46052394,14	K562	blood:
3	chr1:45282552..45286546-chr1:45802804..45805880,5	K562	blood:
4	chr1:45185285..45189072-chr1:45803209..45809453,10	K562	blood:
5	chr1:45803780..45808811-chr1:46047553..46051220,11	K562	blood:
6	chr1:45767877..45774853-chr1:45802459..45807372,12	K562	blood:
7	chr1:45476853..45482658-chr1:45802506..45807966,11	K562	blood:
8	chr1:45483655..45486167-chr1:45802201..45804305,2	K562	blood:
9	chr1:45794537..45798205-chr1:45802201..45806836,5	MCF-7	breast:
10	chr1:45768110..45772204-chr1:45801230..45805942,7	MCF-7	breast:

No data

Variant related genes	Relation type
MUTYH	TF binding region
TOE1	TF binding region
MUTYH	CpG island
TOE1	CpG island
ENSG00000126107	Chromatin interaction
ENSG00000202444	Chromatin interaction
ENSG00000132780	Chromatin interaction
ENSG00000199377	Chromatin interaction
ENSG00000126088	Chromatin interaction
ENSG00000132781	Chromatin interaction
ENSG00000162415	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1548051	1.00[AMR][1000 genomes]
rs16832472	1.00[AMR][1000 genomes]
rs34965970	1.00[AMR][1000 genomes]
rs35210931	1.00[AMR][1000 genomes]
rs56656474	1.00[AMR][1000 genomes]
rs59234831	1.00[AMR][1000 genomes]
rs60338658	1.00[AMR][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	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv1014509	chr1:45687523-45887501	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv997548	chr1:45733596-45955845	Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv534942	chr1:45733596-45955845	Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
5	nsv482356	chr1:45750459-45915545	Enhancers Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
6	esv2750837	chr1:45796115-45908263	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3219473	FKBP7	trans	lymphoblastoid	seeQTL
rs3219473	SYCE1	trans	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45792800-45804800	Weak transcription	Fetal Kidney	kidney
2	chr1:45792800-45805000	Weak transcription	HSMMtube	muscle
3	chr1:45793200-45804800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr1:45793400-45804000	Weak transcription	HMEC	breast
5	chr1:45793400-45805000	Weak transcription	Right Atrium	heart
6	chr1:45793600-45804200	Weak transcription	Fetal Brain Male	brain
7	chr1:45795600-45804400	Weak transcription	A549	lung
8	chr1:45795600-45804800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr1:45795800-45804600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr1:45796400-45804600	Weak transcription	Hela-S3	cervix
11	chr1:45798200-45804400	Weak transcription	Primary hematopoietic stem cells	blood
12	chr1:45798200-45804600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr1:45799000-45804600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr1:45799400-45804600	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr1:45799600-45804200	Weak transcription	Osteobl	bone
16	chr1:45799600-45804400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr1:45799600-45804600	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr1:45799800-45804600	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr1:45799800-45804600	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr1:45799800-45804600	Weak transcription	Fetal Lung	lung
21	chr1:45799800-45804600	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr1:45799800-45804600	Weak transcription	HSMM	muscle
23	chr1:45799800-45804600	Weak transcription	NHLF	lung
24	chr1:45800000-45804400	Weak transcription	Primary B cells from peripheral blood	blood
25	chr1:45800000-45804400	Enhancers	Stomach Mucosa	stomach
26	chr1:45800000-45804600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr1:45800000-45804600	Enhancers	Fetal Intestine Large	intestine
28	chr1:45800000-45804800	Weak transcription	Colon Smooth Muscle	Colon
29	chr1:45800200-45804400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr1:45800200-45804400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr1:45800200-45804400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr1:45800200-45804400	Weak transcription	Brain Germinal Matrix	brain
33	chr1:45800200-45804400	Weak transcription	Fetal Heart	heart
34	chr1:45800200-45804400	Weak transcription	Rectal Smooth Muscle	rectum
35	chr1:45800200-45804600	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr1:45800200-45804600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr1:45800200-45804600	Weak transcription	Brain Anterior Caudate	brain
38	chr1:45800200-45804800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr1:45800200-45805000	Weak transcription	Brain Angular Gyrus	brain
40	chr1:45800200-45805000	Weak transcription	Ovary	ovary
41	chr1:45800400-45804200	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr1:45800400-45804400	Weak transcription	Stomach Smooth Muscle	stomach
43	chr1:45800400-45804600	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr1:45800400-45804600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr1:45800400-45804600	Weak transcription	Gastric	stomach
46	chr1:45800400-45804600	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr1:45800400-45804800	Weak transcription	Primary neutrophils fromperipheralblood	blood
48	chr1:45800400-45805000	Weak transcription	Brain Substantia Nigra	brain
49	chr1:45800400-45805000	Weak transcription	Pancreas	Pancrea
50	chr1:45800600-45804000	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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