Variant report

Variant	rs3893383
Chromosome Location	chr1:45810923-45810924
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:45)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:45 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:45809825-45813195	HepG2	liver:	n/a	n/a
2	POLR2A	chr1:45809707-45813065	GM12892	blood:	n/a	n/a
3	POLR2A	chr1:45809913-45812730	K562	blood:	n/a	n/a
4	POLR2A	chr1:45809778-45813042	GM12891	blood:	n/a	n/a
5	POLR2A	chr1:45809644-45811510	K562	blood:	n/a	n/a
6	POLR2A	chr1:45809815-45812551	HepG2	liver:	n/a	n/a
7	POLR2A	chr1:45810464-45811147	PFSK-1	brain:	n/a	n/a
8	POLR2A	chr1:45809760-45813000	PANC-1	pancreas:	n/a	n/a
9	POLR2A	chr1:45810054-45811445	K562	blood:	n/a	n/a
10	POLR2A	chr1:45810838-45811181	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr1:45809693-45811578	GM12878	blood:	n/a	n/a
12	POLR2A	chr1:45810691-45810931	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr1:45809626-45812792	K562	blood:	n/a	n/a
14	POLR2A	chr1:45810799-45811224	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr1:45809702-45814050	GM12892	blood:	n/a	n/a
16	POLR2A	chr1:45809874-45812853	SK-N-MC	brain:	n/a	n/a
17	POLR2A	chr1:45809781-45812868	GM12878	blood:	n/a	n/a
18	POLR2A	chr1:45810189-45811289	HepG2	liver:	n/a	n/a
19	POLR2A	chr1:45809978-45812732	HepG2	liver:	n/a	n/a
20	POLR2A	chr1:45809789-45812781	GM12891	blood:	n/a	n/a
21	POLR2A	chr1:45810234-45811193	GM19193	blood:	n/a	n/a
22	POLR2A	chr1:45810723-45811527	GM12891	blood:	n/a	n/a
23	POLR2A	chr1:45809848-45813085	GM12891	blood:	n/a	n/a
24	POLR2A	chr1:45809769-45811160	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr1:45807641-45812993	K562	blood:	n/a	n/a
26	POLR2A	chr1:45809963-45815377	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr1:45809891-45812626	PFSK-1	brain:	n/a	n/a
28	POLR2A	chr1:45809863-45811077	K562	blood:	n/a	n/a
29	POLR2A	chr1:45810785-45812852	U87	brain:	n/a	n/a
30	POLR2A	chr1:45810580-45811238	PANC-1	pancreas:	n/a	n/a
31	POLR2A	chr1:45810785-45812856	U87	brain:	n/a	n/a
32	POLR2A	chr1:45809863-45813088	GM12892	blood:	n/a	n/a
33	POLR2A	chr1:45810770-45811226	GM12878	blood:	n/a	n/a
34	POLR2A	chr1:45809899-45814163	K562	blood:	n/a	n/a
35	POLR2A	chr1:45810781-45811245	ECC-1	luminal epithelium:	n/a	n/a
36	POLR2A	chr1:45809940-45811284	Hela-S3	cervix:	n/a	n/a
37	POLR2A	chr1:45809932-45812722	A549	lung:	n/a	n/a
38	POLR2A	chr1:45809822-45813017	GM12892	blood:	n/a	n/a
39	POLR2A	chr1:45809938-45811140	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr1:45809826-45811273	HL-60	blood:	n/a	n/a
41	POLR2A	chr1:45809843-45811630	Hela-S3	cervix:	n/a	n/a
42	POLR2A	chr1:45810138-45811242	GM12878	blood:	n/a	n/a
43	POLR2A	chr1:45809990-45811153	K562	blood:	n/a	n/a
44	POLR2A	chr1:45809851-45813062	K562	blood:	n/a	n/a
45	POLR2A	chr1:45810798-45812662	GM12891	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:45291869..45293559-chr1:45808608..45811445,2	K562	blood:
2	chr1:45575615..45578251-chr1:45809961..45812893,2	K562	blood:
3	chr1:45275803..45277363-chr1:45809748..45811753,2	K562	blood:
4	chr1:45810406..45813503-chr1:45959640..45961736,3	K562	blood:
5	chr1:45478234..45481000-chr1:45809377..45813854,5	K562	blood:
6	chr1:45810813..45813793-chr1:45880439..45883118,2	MCF-7	breast:
7	chr1:45810314..45813113-chr1:46064660..46067353,2	K562	blood:

No data

Variant related genes	Relation type
MUTYH	TF binding region
ENSG00000126088	Chromatin interaction
ENSG00000236872	Chromatin interaction
ENSG00000222009	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs3219495	0.85[LWK][hapmap]
rs56328440	0.82[AFR][1000 genomes]
rs6692066	0.83[AFR][1000 genomes]
rs7535487	0.89[CEU][hapmap];0.89[TSI][hapmap]

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
rs3893383	MUTYH	Cis_1M	lymphoblastoid	RTeQTL
rs3893383	TESK2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45806600-45821600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:45807200-45811000	Strong transcription	H9 Cell Line	embryonic stem cell
3	chr1:45807200-45811200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:45807200-45811200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr1:45807200-45812600	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr1:45807200-45812800	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr1:45807200-45812800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr1:45807200-45814200	Weak transcription	Fetal Brain Male	brain
9	chr1:45807200-45825800	Weak transcription	Small Intestine	intestine
10	chr1:45807400-45811000	Strong transcription	HSMM	muscle
11	chr1:45807400-45811200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:45807400-45811200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
13	chr1:45807400-45811200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr1:45807400-45811600	Strong transcription	A549	lung
15	chr1:45807400-45812400	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr1:45807400-45812800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr1:45807400-45813000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr1:45807400-45813600	Weak transcription	NHDF-Ad	bronchial
19	chr1:45807600-45811000	Strong transcription	NH-A	brain
20	chr1:45807600-45811200	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:45807600-45811200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
22	chr1:45807600-45811200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr1:45807600-45811200	Strong transcription	Ovary	ovary
24	chr1:45807600-45811600	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr1:45807600-45812000	Strong transcription	Fetal Muscle Leg	muscle
26	chr1:45807600-45812200	Strong transcription	H1 Cell Line	embryonic stem cell
27	chr1:45807600-45812600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr1:45807600-45812800	Strong transcription	Rectal Mucosa Donor 31	rectum
29	chr1:45807600-45813400	Weak transcription	Right Atrium	heart
30	chr1:45807800-45811000	Strong transcription	Aorta	Aorta
31	chr1:45807800-45811000	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr1:45807800-45811000	Strong transcription	Osteobl	bone
33	chr1:45807800-45811200	Strong transcription	Brain Germinal Matrix	brain
34	chr1:45807800-45811200	Strong transcription	Esophagus	oesophagus
35	chr1:45807800-45811600	Strong transcription	NHEK	skin
36	chr1:45807800-45811800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr1:45807800-45812000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr1:45807800-45812200	Strong transcription	Brain Substantia Nigra	brain
39	chr1:45807800-45812200	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr1:45807800-45812200	Strong transcription	Sigmoid Colon	Sigmoid Colon
41	chr1:45807800-45812400	Strong transcription	Stomach Smooth Muscle	stomach
42	chr1:45807800-45812600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr1:45807800-45812600	Strong transcription	Brain Anterior Caudate	brain
44	chr1:45807800-45812600	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr1:45807800-45812800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr1:45807800-45812800	Strong transcription	Brain Inferior Temporal Lobe	brain
47	chr1:45807800-45812800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr1:45807800-45812800	Strong transcription	Gastric	stomach
49	chr1:45807800-45812800	Strong transcription	Lung	lung
50	chr1:45807800-45812800	Strong transcription	Thymus	Thymus

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