Variant report

Variant	rs56360441
Chromosome Location	chr2:110370493-110370494
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	chr2:110370191-110373374	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr2:110370338-110372364	HepG2	liver:	n/a	n/a
3	POLR2A	chr2:110370351-110370702	HCT-116	colon:	n/a	n/a
4	FOXA2	chr2:110370457-110370773	HepG2	liver:	n/a	n/a
5	MAFK	chr2:110370347-110371125	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr2:110370230-110370868	PANC-1	pancreas:	n/a	n/a
7	RFX5	chr2:110370354-110372172	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr2:110369085-110379088	Hela-S3	cervix:	n/a	n/a
9	RAD21	chr2:110370439-110370718	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr2:110370305-110374042	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr2:110370315-110373849	Hela-S3	cervix:	n/a	n/a
12	ARID3A	chr2:110369207-110370805	HepG2	liver:	n/a	n/a
13	BRCA1	chr2:110369558-110370993	Hela-S3	cervix:	n/a	n/a
14	ZNF263	chr2:110370375-110374014	HEK293-T-REx	kidney:	n/a	n/a
15	POLR2A	chr2:110370486-110372160	HUVEC	blood vessel:	n/a	n/a
16	POLR2A	chr2:110369276-110373158	IMR90	lung:	n/a	n/a
17	E2F4	chr2:110369413-110372380	MCF10A-Er-Src	breast:	n/a	chr2:110371142-110371152 chr2:110370860-110370874 chr2:110370863-110370870 chr2:110370862-110370871 chr2:110370863-110370870 chr2:110370863-110370870 chr2:110370859-110370871 chr2:110371199-110371211 chr2:110370968-110370978 chr2:110371209-110371219 chr2:110371309-110371321
18	RCOR1	chr2:110370377-110372209	HepG2	liver:	n/a	n/a
19	POLR2A	chr2:110369422-110372500	Hela-S3	cervix:	n/a	n/a
20	MXI1	chr2:110370313-110372007	GM12878	blood:	n/a	n/a
21	POLR2A	chr2:110370120-110370665	HUVEC	blood vessel:	n/a	n/a
22	POLR2A	chr2:110369410-110372842	MCF10A-Er-Src	breast:	n/a	n/a
23	CHD1	chr2:110370250-110371750	GM12878	blood:	n/a	n/a
24	CHD1	chr2:110369172-110374773	IMR90	lung:	n/a	n/a
25	POLR2A	chr2:110370314-110370573	Hela-S3	cervix:	n/a	n/a
26	MXI1	chr2:110370220-110373217	IMR90	lung:	n/a	n/a
27	TBP	chr2:110370342-110371175	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr2:110369290-110378742	MCF10A-Er-Src	breast:	n/a	n/a
29	MAZ	chr2:110370358-110373280	IMR90	lung:	n/a	n/a
30	GTF2F1	chr2:110370385-110371038	Hela-S3	cervix:	n/a	n/a
31	HCFC1	chr2:110370323-110372164	Hela-S3	cervix:	n/a	n/a
32	MAZ	chr2:110370439-110372084	GM12878	blood:	n/a	n/a
33	STAT3	chr2:110370401-110370593	MCF10A-Er-Src	breast:	n/a	n/a
34	CHD1	chr2:110370075-110371212	H1-hESC	embryonic stem cell:	n/a	n/a
35	MXI1	chr2:110370146-110372839	SK-N-SH	brain:	n/a	n/a
36	MYC	chr2:110370442-110373695	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:110362640..110365155-chr2:110368934..110372656,4	MCF-7	breast:
2	chr2:110368286..110370966-chr2:110371073..110372751,2	MCF-7	breast:
3	chr1:150131401..150134100-chr2:110369407..110372211,2	MCF-7	breast:

Variant related genes	Relation type
SOWAHC	TF binding region
ENSG00000186522	Chromatin interaction
ENSG00000230696	Chromatin interaction
ENSG00000023902	Chromatin interaction
ENSG00000198142	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs56195919	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6705280	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73953161	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73953934	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874777	chr2:109825516-110693317	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv874780	chr2:110078080-110432886	Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1011456	chr2:110290958-110980402	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv535861	chr2:110290958-110980402	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv482469	chr2:110302488-110452580	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv1009367	chr2:110349178-110863354	Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
7	nsv829617	chr2:110359857-110380012	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
8	esv2762780	chr2:110367969-110462496	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:110359800-110370600	Weak transcription	Brain Angular Gyrus	brain
2	chr2:110368000-110370800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:110368600-110371200	Active TSS	GM12878-XiMat	blood
4	chr2:110369000-110373000	Active TSS	NHLF	lung
5	chr2:110369000-110373800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr2:110369200-110370600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr2:110369200-110370600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr2:110369400-110370600	Flanking Active TSS	Brain Germinal Matrix	brain
9	chr2:110369400-110370600	Weak transcription	Lung	lung
10	chr2:110369400-110370600	Flanking Active TSS	Rectal Smooth Muscle	rectum
11	chr2:110369400-110372000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr2:110369400-110372400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr2:110369400-110372400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr2:110369400-110372600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr2:110369400-110373200	Active TSS	HSMM	muscle
16	chr2:110369400-110374600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr2:110369600-110370600	Flanking Active TSS	Stomach Smooth Muscle	stomach
18	chr2:110369600-110371800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr2:110369600-110372600	Active TSS	Right Atrium	heart
20	chr2:110369600-110372800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr2:110369600-110373800	Active TSS	Aorta	Aorta
22	chr2:110369600-110374000	Active TSS	Hela-S3	cervix
23	chr2:110369800-110370600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
24	chr2:110369800-110370600	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr2:110369800-110371000	Flanking Active TSS	Fetal Brain Female	brain
26	chr2:110369800-110372600	Active TSS	ES-I3 Cell Line	embryonic stem cell
27	chr2:110369800-110373400	Active TSS	A549	lung
28	chr2:110369800-110374200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr2:110370000-110370600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
30	chr2:110370000-110372200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr2:110370000-110372400	Active TSS	Right Ventricle	heart
32	chr2:110370000-110372600	Active TSS	H1 Cell Line	embryonic stem cell
33	chr2:110370000-110372600	Active TSS	iPS-18 Cell Line	embryonic stem cell
34	chr2:110370000-110372600	Active TSS	iPS-20b Cell Line	embryonic stem cell
35	chr2:110370000-110372600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
36	chr2:110370000-110372600	Active TSS	Fetal Stomach	stomach
37	chr2:110370000-110372600	Active TSS	Ovary	ovary
38	chr2:110370000-110372600	Active TSS	HMEC	breast
39	chr2:110370000-110372800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr2:110370000-110372800	Active TSS	Rectal Mucosa Donor 31	rectum
41	chr2:110370000-110373000	Active TSS	NHDF-Ad	bronchial
42	chr2:110370000-110373800	Active TSS	H9 Cell Line	embryonic stem cell
43	chr2:110370000-110373800	Active TSS	Pancreatic Islets	Pancreatic Islet
44	chr2:110370000-110374000	Active TSS	Fetal Kidney	kidney
45	chr2:110370000-110374800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr2:110370000-110375000	Active TSS	NHEK	skin
47	chr2:110370200-110370600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
48	chr2:110370200-110370600	Flanking Active TSS	Brain Cingulate Gyrus	brain
49	chr2:110370200-110370600	Flanking Active TSS	Brain Hippocampus Middle	brain
50	chr2:110370200-110370600	Flanking Active TSS	Fetal Muscle Leg	muscle

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