Variant report

Variant	rs56122560
Chromosome Location	chr3:50316007-50316008
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:23)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:23 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:50315920-50316425	HepG2	liver:	n/a	n/a
2	POLR2A	chr3:50315553-50317405	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr3:50315302-50317402	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr3:50315397-50317356	HepG2	liver:	n/a	n/a
5	POLR2A	chr3:50315300-50317392	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr3:50315907-50316133	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr3:50313950-50317579	HepG2	liver:	n/a	n/a
8	MYC	chr3:50315800-50316063	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr3:50315535-50317282	Hela-S3	cervix:	n/a	n/a
10	FOSL2	chr3:50315899-50316446	HepG2	liver:	n/a	n/a
11	POLR2A	chr3:50315412-50316374	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr3:50315909-50316129	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr3:50315554-50316214	MCF10A-Er-Src	breast:	n/a	n/a
14	POLR2A	chr3:50315260-50316356	HepG2	liver:	n/a	n/a
15	POLR2A	chr3:50315475-50317172	HepG2	liver:	n/a	n/a
16	POLR2A	chr3:50315328-50317396	ECC-1	luminal epithelium:	n/a	n/a
17	POLR2A	chr3:50315423-50316243	HepG2	liver:	n/a	n/a
18	POLR2A	chr3:50315901-50316241	HCT-116	colon:	n/a	n/a
19	POLR2A	chr3:50315397-50317323	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr3:50315078-50317415	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr3:50315413-50317240	HepG2	liver:	n/a	n/a
22	POLR2A	chr3:50315430-50317250	A549	lung:	n/a	n/a
23	POLR2A	chr3:50315777-50317368	ECC-1	luminal epithelium:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:50305641..50310504-chr3:50314554..50317584,4	K562	blood:
2	chr3:50307758..50309576-chr3:50315443..50317608,2	MCF-7	breast:
3	chr3:50315023..50318386-chr3:50356939..50360295,5	MCF-7	breast:
4	chr3:50274207..50276620-chr3:50314026..50316951,2	MCF-7	breast:
5	chr3:50315763..50317890-chr3:50327767..50331626,3	K562	blood:
6	chr3:50296030..50318456-chr3:50318822..50339499,66	MCF-7	breast:
7	chr3:50314390..50316856-chr3:50357107..50359753,2	MCF-7	breast:
8	chr3:50283654..50286380-chr3:50314106..50317023,3	K562	blood:
9	chr3:50310650..50313903-chr3:50314125..50318251,8	MCF-7	breast:

No data

Variant related genes	Relation type
LSMEM2	TF binding region
ENSG00000243477	Chromatin interaction
ENSG00000114353	Chromatin interaction
ENSG00000012171	Chromatin interaction
ENSG00000214706	Chromatin interaction
ENSG00000186792	Chromatin interaction
ENSG00000068001	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs2298952	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9832454	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:30 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv523662	chr3:50144951-50584999	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	nsv1013949	chr3:50151712-50339163	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
3	nsv590250	chr3:50153356-50332697	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv876769	chr3:50155468-50408398	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
5	esv1821728	chr3:50156142-50657253	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
6	esv1793751	chr3:50157364-50476363	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
7	esv1828162	chr3:50157364-50506151	Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
8	nsv590251	chr3:50158774-50337422	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
9	nsv470561	chr3:50158774-50584999	Flanking Active TSS Enhancers Weak transcription Genic enhancers 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	99 gene(s)	inside rSNPs	diseases
10	nsv876770	chr3:50158774-50609624	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
11	nsv523560	chr3:50172397-50339163	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription 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	53 gene(s)	inside rSNPs	diseases
12	nsv460529	chr3:50178011-50324672	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
13	nsv460530	chr3:50178011-50324672	Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
14	nsv590252	chr3:50178011-50324672	Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
15	nsv1014256	chr3:50187646-50339163	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
16	nsv536565	chr3:50187646-50339163	Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Enhancers Weak transcription Genic enhancers 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 miRNA target site	53 gene(s)	inside rSNPs	diseases
17	nsv1001993	chr3:50187646-50640808	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription 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	104 gene(s)	inside rSNPs	diseases
18	nsv590253	chr3:50196418-50337422	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
19	esv2757870	chr3:50198478-50371377	Genic enhancers Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
20	esv2759148	chr3:50198478-50371377	Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
21	nsv834692	chr3:50198485-50393464	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
22	nsv590254	chr3:50243510-50388607	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
23	nsv460531	chr3:50247824-50436827	Strong transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
24	nsv590255	chr3:50247824-50436827	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
25	nsv876772	chr3:50255305-50436827	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
26	nsv590257	chr3:50302830-50393640	Genic enhancers Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
27	nsv590256	chr3:50302830-50420554	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
28	nsv876774	chr3:50302830-50436827	Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
29	nsv876773	chr3:50302830-50480131	Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
30	nsv834693	chr3:50302830-50507964	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50310800-50325800	Weak transcription	HSMM	muscle
2	chr3:50311000-50316200	Weak transcription	Colon Smooth Muscle	Colon
3	chr3:50311000-50323400	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr3:50311200-50323400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr3:50311800-50324400	Weak transcription	HMEC	breast
6	chr3:50312200-50323200	Weak transcription	A549	lung
7	chr3:50312200-50323400	Weak transcription	Lung	lung
8	chr3:50312200-50324000	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr3:50312200-50325600	Weak transcription	K562	blood
10	chr3:50312800-50316200	Strong transcription	Gastric	stomach
11	chr3:50313800-50323400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr3:50314000-50323800	Weak transcription	Liver	Liver
13	chr3:50314200-50323200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr3:50314200-50323800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr3:50314200-50324000	Weak transcription	Colonic Mucosa	Colon
16	chr3:50314200-50324000	Weak transcription	Pancreas	Pancrea
17	chr3:50314600-50316200	Strong transcription	Placenta	Placenta
18	chr3:50314600-50317200	Strong transcription	Fetal Intestine Small	intestine
19	chr3:50314600-50323800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr3:50314600-50324000	Weak transcription	Adipose Nuclei	Adipose
21	chr3:50314600-50324600	Weak transcription	Hela-S3	cervix
22	chr3:50314600-50325000	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr3:50314800-50316400	Strong transcription	Fetal Intestine Large	intestine
24	chr3:50314800-50324000	Weak transcription	Ovary	ovary
25	chr3:50315400-50316400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
26	chr3:50315400-50316400	Enhancers	Stomach Smooth Muscle	stomach
27	chr3:50315400-50316800	Enhancers	Right Ventricle	heart
28	chr3:50315400-50317200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr3:50315400-50317200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
30	chr3:50315400-50317400	Enhancers	Brain Substantia Nigra	brain
31	chr3:50315600-50316200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr3:50315600-50316400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr3:50315600-50316400	Enhancers	Left Ventricle	heart
34	chr3:50315600-50316600	Enhancers	Right Atrium	heart
35	chr3:50315600-50317400	Enhancers	Brain Inferior Temporal Lobe	brain
36	chr3:50315600-50317400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
37	chr3:50315600-50324000	Weak transcription	Esophagus	oesophagus
38	chr3:50315800-50316400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:50315800-50316600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr3:50315800-50316600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr3:50315800-50316600	Enhancers	Fetal Muscle Leg	muscle
42	chr3:50315800-50317000	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr3:50315800-50317200	Enhancers	Psoas Muscle	Psoas
44	chr3:50315800-50317200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
45	chr3:50315800-50324000	Weak transcription	Duodenum Mucosa	Duodenum
46	chr3:50316000-50316200	Flanking Active TSS	Brain Hippocampus Middle	brain
47	chr3:50316000-50316200	Enhancers	Duodenum Smooth Muscle	Duodenum
48	chr3:50316000-50316400	Enhancers	HepG2	liver
49	chr3:50316000-50316600	Enhancers	Aorta	Aorta
50	chr3:50316000-50316600	Enhancers	Brain Anterior Caudate	brain

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