Variant report

Variant	rs36116071
Chromosome Location	chr3:49706699-49706700
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:12)
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	POLR2A	chr3:49706657-49707108	HL-60	blood:	n/a	n/a
2	POLR2A	chr3:49706485-49706848	MCF-7	breast:	n/a	n/a
3	MAX	chr3:49706313-49706732	ECC-1	luminal epithelium:	n/a	n/a
4	POLR2A	chr3:49706418-49708747	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr3:49706371-49707153	ECC-1	luminal epithelium:	n/a	n/a
6	POLR2A	chr3:49706617-49707043	K562	blood:	n/a	n/a
7	POLR2A	chr3:49706402-49706764	HCT-116	colon:	n/a	n/a
8	FOSL2	chr3:49706280-49706750	A549	lung:	n/a	n/a
9	POLR2A	chr3:49706612-49706903	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr3:49706501-49707090	HepG2	liver:	n/a	n/a
11	POLR2A	chr3:49706366-49708956	K562	blood:	n/a	n/a
12	POLR2A	chr3:49706691-49706867	MCF10A-Er-Src	breast:	n/a	n/a
13	FOSL2	chr3:49706295-49706703	MCF-7	breast:	n/a	n/a
14	POLR2A	chr3:49706617-49707126	PANC-1	pancreas:	n/a	n/a
15	REST	chr3:49706579-49706846	PANC-1	pancreas:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:49698247..49700593-chr3:49704782..49707775,2	MCF-7	breast:
2	chr3:49588369..49592998-chr3:49704328..49708705,5	K562	blood:
3	chr3:49704547..49706836-chr3:49714459..49716398,2	MCF-7	breast:
4	chr3:49588369..49590572-chr3:49704819..49707525,2	K562	blood:
5	chr3:49591933..49593774-chr3:49706277..49708341,2	MCF-7	breast:
6	chr3:49577520..49579267-chr3:49706031..49707871,2	MCF-7	breast:
7	chr3:49576201..49578760-chr3:49706386..49709294,3	MCF-7	breast:
8	chr3:49704645..49708091-chr3:49709856..49713074,5	MCF-7	breast:
9	chr3:49598290..49599982-chr3:49704902..49707508,2	MCF-7	breast:
10	chr3:49507427..49510910-chr3:49706254..49709319,3	MCF-7	breast:
11	chr3:49701796..49704696-chr3:49705542..49707912,3	MCF-7	breast:
12	chr3:49694199..49696259-chr3:49706473..49708487,2	MCF-7	breast:

No data

Variant related genes	Relation type
APEH	TF binding region
ENSG00000164062	Chromatin interaction
ENSG00000173402	Chromatin interaction
ENSG00000164061	Chromatin interaction
ENSG00000226913	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs13061156	0.87[AMR][1000 genomes]
rs13071087	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13100791	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3206653	0.87[AMR][1000 genomes]
rs35620248	0.87[AMR][1000 genomes]
rs71324984	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71324987	0.87[AMR][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	nsv508217	chr3:49615446-49769896	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	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
3	esv1825898	chr3:49688948-49764849	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
4	esv1808511	chr3:49689880-49744825	Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49685200-49708200	Strong transcription	Brain Germinal Matrix	brain
2	chr3:49685400-49708400	Strong transcription	Fetal Brain Female	brain
3	chr3:49686600-49710600	Weak transcription	Right Atrium	heart
4	chr3:49690400-49710600	Weak transcription	Brain Substantia Nigra	brain
5	chr3:49692200-49710400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:49695200-49710600	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr3:49700000-49710600	Weak transcription	Fetal Brain Male	brain
8	chr3:49701800-49707000	Enhancers	Fetal Muscle Leg	muscle
9	chr3:49702000-49707400	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr3:49702400-49710600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:49702800-49707400	Enhancers	Pancreas	Pancrea
12	chr3:49703400-49709400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr3:49703600-49709000	Weak transcription	Placenta	Placenta
14	chr3:49703600-49710600	Weak transcription	Left Ventricle	heart
15	chr3:49703600-49710600	Weak transcription	Right Ventricle	heart
16	chr3:49703600-49710600	Weak transcription	Spleen	Spleen
17	chr3:49703800-49710600	Enhancers	Liver	Liver
18	chr3:49703800-49710600	Weak transcription	Brain Hippocampus Middle	brain
19	chr3:49704000-49706800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr3:49704000-49707000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr3:49704200-49710600	Weak transcription	Gastric	stomach
22	chr3:49704400-49710600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr3:49704600-49709000	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr3:49704600-49709400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr3:49704600-49710600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr3:49704600-49710600	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr3:49704800-49710600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr3:49705000-49707000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
29	chr3:49705000-49710600	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr3:49705200-49707200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr3:49705200-49707200	Enhancers	A549	lung
32	chr3:49705200-49708400	Enhancers	HepG2	liver
33	chr3:49705400-49707000	Enhancers	Muscle Satellite Cultured Cells	--
34	chr3:49705400-49707000	Enhancers	Placenta Amnion	Placenta Amnion
35	chr3:49705400-49707200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr3:49705400-49707200	Enhancers	HMEC	breast
37	chr3:49705400-49709000	Weak transcription	Brain Cingulate Gyrus	brain
38	chr3:49705600-49706800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr3:49705600-49706800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr3:49705600-49706800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr3:49705600-49707000	Enhancers	Adipose Nuclei	Adipose
42	chr3:49705600-49707000	Enhancers	HSMM	muscle
43	chr3:49705600-49707000	Enhancers	NH-A	brain
44	chr3:49705600-49707200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr3:49705600-49710600	Weak transcription	Brain Anterior Caudate	brain
46	chr3:49705600-49710600	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr3:49705600-49710600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr3:49705800-49706800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr3:49705800-49707000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr3:49705800-49707000	Enhancers	Hela-S3	cervix

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