Variant report

Variant	rs56352827
Chromosome Location	chr3:49920297-49920298
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:49919982-49920447	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr3:49916166-49923391	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr3:49917897-49920397	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr3:49918314-49920607	HCT-116	colon:	n/a	n/a
5	POLR2A	chr3:49911230-49922975	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr3:49917041-49920433	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr3:49918306-49920583	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:49920014..49922946-chr3:49924435..49926643,2	K562	blood:
2	chr3:49917501..49919424-chr3:49920193..49922389,2	K562	blood:
3	chr3:49918459..49920341-chr3:49922556..49924105,2	K562	blood:
4	chr3:49918643..49920553-chr3:49922837..49925319,3	MCF-7	breast:

Variant related genes	Relation type
ACTBP13	TF binding region

Extended variants
information (count: 16 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs2230592	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28424211	0.87[AFR][1000 genomes]
rs35340753	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56057035	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57347154	0.87[AFR][1000 genomes]
rs61156427	0.87[AFR][1000 genomes]
rs73831918	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73832783	0.87[AFR][1000 genomes]
rs73834119	0.87[AFR][1000 genomes]
rs73834125	0.87[AFR][1000 genomes]
rs73834127	0.87[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	esv1809827	chr3:49812331-49934179	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	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
5	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:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49917200-49920400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
2	chr3:49917800-49920400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:49918000-49920400	Enhancers	Left Ventricle	heart
4	chr3:49918200-49920400	Enhancers	Placenta	Placenta
5	chr3:49918600-49920400	Bivalent Enhancer	Adipose Nuclei	Adipose
6	chr3:49918800-49920400	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr3:49918800-49928400	Weak transcription	Colonic Mucosa	Colon
8	chr3:49919000-49920400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
9	chr3:49919000-49920400	Bivalent Enhancer	HepG2	liver
10	chr3:49919000-49924000	Weak transcription	Gastric	stomach
11	chr3:49919000-49924000	Weak transcription	Lung	lung
12	chr3:49919000-49924200	Weak transcription	Hela-S3	cervix
13	chr3:49919400-49924000	Weak transcription	K562	blood
14	chr3:49919400-49924200	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr3:49919400-49928600	Weak transcription	Esophagus	oesophagus
16	chr3:49919600-49924000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr3:49919600-49924000	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr3:49919600-49926400	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr3:49919600-49933400	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr3:49919600-49933400	Weak transcription	Stomach Mucosa	stomach
21	chr3:49919600-49937800	Weak transcription	Small Intestine	intestine
22	chr3:49919800-49924000	Weak transcription	NHEK	skin
23	chr3:49919800-49926600	Weak transcription	Spleen	Spleen
24	chr3:49919800-49933800	Weak transcription	Brain Angular Gyrus	brain
25	chr3:49920000-49920400	Enhancers	Fetal Brain Male	brain
26	chr3:49920000-49920400	Enhancers	Fetal Lung	lung
27	chr3:49920000-49920600	Enhancers	Skeletal Muscle Male	skeletal muscle
28	chr3:49920000-49924000	Weak transcription	Duodenum Mucosa	Duodenum
29	chr3:49920000-49924000	Weak transcription	Fetal Brain Female	brain
30	chr3:49920000-49926200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr3:49920000-49930200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr3:49920000-49943000	Weak transcription	Brain Anterior Caudate	brain
33	chr3:49920200-49920400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr3:49920200-49920600	Enhancers	Fetal Muscle Leg	muscle
35	chr3:49920200-49921000	Weak transcription	Fetal Intestine Large	intestine
36	chr3:49920200-49921000	Weak transcription	Fetal Intestine Small	intestine
37	chr3:49920200-49924000	Weak transcription	Fetal Stomach	stomach
38	chr3:49920200-49924200	Weak transcription	Right Atrium	heart
39	chr3:49920200-49932600	Weak transcription	Rectal Smooth Muscle	rectum
40	chr3:49920200-49932600	Weak transcription	Stomach Smooth Muscle	stomach
41	chr3:49920200-49938400	Weak transcription	Duodenum Smooth Muscle	Duodenum

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