Variant report

Variant	rs13318943
Chromosome Location	chr3:49940499-49940500
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:15 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr3:49940085-49941672	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr3:49939501-49941825	HCT-116	colon:	n/a	n/a
3	POLR2A	chr3:49940201-49940747	Hela-S3	cervix:	n/a	n/a
4	CEBPB	chr3:49940329-49940968	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr3:49939484-49941805	Hela-S3	cervix:	n/a	n/a
6	SIN3AK20	chr3:49940473-49941824	HCT-116	colon:	n/a	n/a
7	POLR2A	chr3:49940263-49941748	Hela-S3	cervix:	n/a	n/a
8	MXI1	chr3:49940107-49940515	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr3:49940360-49940702	K562	blood:	n/a	n/a
10	POLR2A	chr3:49940276-49941638	Hela-S3	cervix:	n/a	n/a
11	RCOR1	chr3:49940208-49940830	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr3:49939864-49941766	HCT-116	colon:	n/a	n/a
13	RFX5	chr3:49940199-49940519	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr3:49939517-49941790	Hela-S3	cervix:	n/a	n/a
15	SMARCB1	chr3:49939531-49941759	Hela-S3	cervix:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr3:49907025..49909566-chr3:49939184..49940917,2	K562	blood:
2	chr19:2475693..2476461-chr3:49939604..49940586,2	Hela-S3	cervix:
3	chr3:49844713..49846618-chr3:49938018..49940554,2	K562	blood:
4	chr17:57914844..57915614-chr3:49940402..49941042,2	Hela-S3	cervix:
5	chr3:49936090..49937594-chr3:49939320..49940938,2	K562	blood:
6	chr3:49837665..49841605-chr3:49939148..49941365,3	K562	blood:
7	chr3:49933351..49938041-chr3:49938966..49942332,9	K562	blood:

No data

Variant related genes	Relation type
ENSG00000228008	TF binding region
ENSG00000185614	Chromatin interaction
ENSG00000164078	Chromatin interaction
ENSG00000099860	Chromatin interaction
ENSG00000062716	Chromatin interaction
ENSG00000230698	Chromatin interaction
ENSG00000164076	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs12330297	1.00[AFR][1000 genomes]
rs13316958	0.87[AFR][1000 genomes]
rs13323932	0.87[AFR][1000 genomes]
rs13324545	1.00[AFR][1000 genomes]
rs55968312	1.00[AFR][1000 genomes]
rs9811223	0.87[AFR][1000 genomes]
rs9819888	1.00[AFR][1000 genomes]
rs9825944	1.00[AFR][1000 genomes]
rs9828683	1.00[AFR][1000 genomes]
rs9835029	1.00[AFR][1000 genomes]
rs9835838	0.87[AFR][1000 genomes]
rs9849605	1.00[AFR][1000 genomes]
rs9850145	0.87[AFR][1000 genomes]
rs9852055	0.86[AFR][1000 genomes]
rs9862830	1.00[AFR][1000 genomes]
rs9863339	1.00[AFR][1000 genomes]
rs9864231	1.00[AFR][1000 genomes]
rs9866016	1.00[AFR][1000 genomes]
rs9875038	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1796352	chr3:49687101-49949959	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv834688	chr3:49811115-50019299	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	nsv876766	chr3:49817450-49961780	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv876767	chr3:49918751-50153356	Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49920000-49943000	Weak transcription	Brain Anterior Caudate	brain
2	chr3:49925200-49941200	Weak transcription	Brain Germinal Matrix	brain
3	chr3:49928600-49943000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr3:49929600-49941200	Weak transcription	Ovary	ovary
5	chr3:49931400-49943600	Weak transcription	Brain Hippocampus Middle	brain
6	chr3:49933800-49941400	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr3:49934400-49941400	Weak transcription	Brain Angular Gyrus	brain
8	chr3:49936200-49941000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr3:49936400-49940800	Enhancers	Pancreas	Pancrea
10	chr3:49937000-49940800	Enhancers	Sigmoid Colon	Sigmoid Colon
11	chr3:49937600-49940800	Enhancers	K562	blood
12	chr3:49937600-49941000	Enhancers	Placenta	Placenta
13	chr3:49937600-49943200	Active TSS	Rectal Smooth Muscle	rectum
14	chr3:49938000-49941400	Enhancers	GM12878-XiMat	blood
15	chr3:49938200-49940600	Enhancers	Fetal Stomach	stomach
16	chr3:49938200-49940800	Enhancers	Fetal Muscle Leg	muscle
17	chr3:49938200-49941800	Flanking Active TSS	HMEC	breast
18	chr3:49938400-49940800	Enhancers	Colon Smooth Muscle	Colon
19	chr3:49938400-49941000	Enhancers	Fetal Muscle Trunk	muscle
20	chr3:49938600-49941200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr3:49938800-49940600	Enhancers	A549	lung
22	chr3:49938800-49940800	Weak transcription	Left Ventricle	heart
23	chr3:49938800-49941000	Weak transcription	Psoas Muscle	Psoas
24	chr3:49938800-49943200	Weak transcription	HSMMtube	muscle
25	chr3:49938800-49943200	Weak transcription	NH-A	brain
26	chr3:49939000-49941000	Weak transcription	Osteobl	bone
27	chr3:49939000-49941200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr3:49939000-49941200	Weak transcription	NHLF	lung
29	chr3:49939000-49941400	Active TSS	Hela-S3	cervix
30	chr3:49939000-49941600	Active TSS	Duodenum Smooth Muscle	Duodenum
31	chr3:49939000-49943200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr3:49939000-49943200	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr3:49939000-49943400	Weak transcription	HSMM	muscle
34	chr3:49939200-49940800	Enhancers	Fetal Thymus	thymus
35	chr3:49939200-49941000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr3:49939200-49941000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr3:49939200-49941200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr3:49939200-49941400	Weak transcription	NHDF-Ad	bronchial
39	chr3:49939400-49940600	Enhancers	Lung	lung
40	chr3:49939400-49940800	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr3:49939400-49940800	Flanking Active TSS	Esophagus	oesophagus
42	chr3:49939400-49940800	Weak transcription	Small Intestine	intestine
43	chr3:49939400-49940800	Transcr. at gene 5' and 3'	NHEK	skin
44	chr3:49939400-49941800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
45	chr3:49939400-49942200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
46	chr3:49939400-49943400	Weak transcription	Brain Cingulate Gyrus	brain
47	chr3:49939600-49940800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr3:49939600-49940800	Strong transcription	Fetal Brain Female	brain
49	chr3:49939600-49941000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr3:49939600-49941400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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