Variant report

Variant	rs2903838
Chromosome Location	chr2:56150402-56150403
allele	A/G
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	E2F6	chr2:56150261-56151205	H1-hESC	embryonic stem cell:	n/a	chr2:56150780-56150792 chr2:56151077-56151086 chr2:56151106-56151116 chr2:56151102-56151114
2	MXI1	chr2:56149060-56151667	IMR90	lung:	n/a	n/a
3	MAZ	chr2:56150309-56151220	Hela-S3	cervix:	n/a	chr2:56151182-56151193
4	E2F6	chr2:56150318-56151274	A549	lung:	n/a	chr2:56150780-56150792 chr2:56151077-56151086 chr2:56151106-56151116 chr2:56151102-56151114
5	POLR2A	chr2:56150230-56150970	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr2:56150388-56151034	MCF10A-Er-Src	breast:	n/a	n/a
7	SMC3	chr2:56150325-56151245	Hela-S3	cervix:	n/a	chr2:56151079-56151089
8	POLR2A	chr2:56149657-56151154	MCF10A-Er-Src	breast:	n/a	n/a
9	EP300	chr2:56150321-56151384	SK-N-SH	brain:	n/a	n/a
10	CTBP2	chr2:56150129-56151225	H1-hESC	embryonic stem cell:	n/a	n/a
11	TCF12	chr2:56150371-56151103	A549	lung:	n/a	chr2:56150532-56150539
12	SIN3AK20	chr2:56150399-56151097	SK-N-SH	brain:	n/a	n/a
13	MAX	chr2:56150402-56151434	A549	lung:	n/a	chr2:56151182-56151193
14	TBP	chr2:56150321-56151350	H1-hESC	embryonic stem cell:	n/a	n/a
15	TEAD4	chr2:56150283-56151351	SK-N-SH	brain:	n/a	n/a
16	MAX	chr2:56150347-56151381	SK-N-SH	brain:	n/a	chr2:56151182-56151193
17	MYC	chr2:56150297-56150922	MCF10A-Er-Src	breast:	n/a	n/a
18	MXI1	chr2:56150053-56150850	Hela-S3	cervix:	n/a	n/a
19	MAX	chr2:56149561-56151225	H1-hESC	embryonic stem cell:	n/a	chr2:56151182-56151193
20	TEAD4	chr2:56150395-56151205	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr2:56150377-56151150	MCF-7	breast:	n/a	n/a
22	MAX	chr2:56150242-56151278	H1-hESC	embryonic stem cell:	n/a	chr2:56151182-56151193
23	TAF1	chr2:56149537-56150532	H1-hESC	embryonic stem cell:	n/a	n/a
24	CTCF	chr2:56150340-56150490	A549	lung:	n/a	n/a
25	SIN3A	chr2:56149537-56151428	H1-hESC	embryonic stem cell:	n/a	chr2:56150484-56150493
26	POLR2A	chr2:56146785-56151297	HUVEC	blood vessel:	n/a	n/a
27	FOXP2	chr2:56150344-56151246	PFSK-1	brain:	n/a	n/a
28	MAX	chr2:56150219-56151266	H1-hESC	embryonic stem cell:	n/a	chr2:56151182-56151193
29	POLR2A	chr2:56148670-56151244	IMR90	lung:	n/a	n/a
30	TCF7L2	chr2:56149642-56150948	Hela-S3	cervix:	n/a	n/a
31	POLR2A	chr2:56149464-56151265	HUVEC	blood vessel:	n/a	n/a
32	POLR2A	chr2:56133504-56151767	HUVEC	blood vessel:	n/a	n/a
33	MAX	chr2:56150105-56151481	A549	lung:	n/a	chr2:56151182-56151193
34	RAD21	chr2:56150163-56151199	IMR90	lung:	n/a	chr2:56151079-56151089
35	POLR2A	chr2:56149436-56151158	H1-hESC	embryonic stem cell:	n/a	n/a
36	RCOR1	chr2:56150317-56151502	Hela-S3	cervix:	n/a	n/a
37	MAX	chr2:56150344-56151204	MCF-7	breast:	n/a	chr2:56151182-56151193
38	MAX	chr2:56150359-56151350	SK-N-SH	brain:	n/a	chr2:56151182-56151193
39	POLR2A	chr2:56147841-56151285	HUVEC	blood vessel:	n/a	n/a
40	POLR2A	chr2:56150401-56151287	MCF-7	breast:	n/a	n/a
41	POLR2A	chr2:56148537-56151190	HUVEC	blood vessel:	n/a	n/a
42	MAZ	chr2:56149218-56151848	IMR90	lung:	n/a	chr2:56151182-56151193
43	RAD21	chr2:56150373-56151189	A549	lung:	n/a	chr2:56151079-56151089
44	BACH1	chr2:56149616-56151221	H1-hESC	embryonic stem cell:	n/a	n/a
45	POLR2A	chr2:56148511-56151263	HUVEC	blood vessel:	n/a	n/a
46	JUND	chr2:56149964-56150406	H1-hESC	embryonic stem cell:	n/a	chr2:56150188-56150199
47	MAFK	chr2:56150174-56151281	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
EFEMP1	TF binding region

Extended variants
information (count: 9 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10192203	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2033316	1.00[CHB][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs2868435	1.00[CHB][hapmap]
rs3762515	1.00[CHB][hapmap]
rs4233964	1.00[CHB][hapmap]
rs7608756	0.87[AMR][1000 genomes]
rs960993	1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531374	chr2:55653723-56299784	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	esv3430118	chr2:56147911-56152306	Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:56147400-56151400	Active TSS	Aorta	Aorta
2	chr2:56148600-56151400	Flanking Active TSS	Adipose Nuclei	Adipose
3	chr2:56148600-56151600	Active TSS	Right Atrium	heart
4	chr2:56148800-56151400	Active TSS	Brain Anterior Caudate	brain
5	chr2:56149000-56151200	Active TSS	Colon Smooth Muscle	Colon
6	chr2:56149000-56151400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr2:56149000-56151400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
8	chr2:56149000-56151400	Active TSS	Ovary	ovary
9	chr2:56149000-56151400	Active TSS	HSMMtube	muscle
10	chr2:56149200-56151000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr2:56149200-56151200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
12	chr2:56149200-56151200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
13	chr2:56149200-56151200	Bivalent/Poised TSS	NHDF-Ad	bronchial
14	chr2:56149200-56151400	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
15	chr2:56149200-56151400	Active TSS	Brain Cingulate Gyrus	brain
16	chr2:56149200-56151600	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
17	chr2:56149400-56150600	Active TSS	H9 Cell Line	embryonic stem cell
18	chr2:56149400-56151000	Bivalent/Poised TSS	Left Ventricle	heart
19	chr2:56149400-56151000	Active TSS	Lung	lung
20	chr2:56149400-56151200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
21	chr2:56149400-56151200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr2:56149400-56151400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr2:56149400-56151400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr2:56149400-56151400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
25	chr2:56149400-56151400	Active TSS	Brain Substantia Nigra	brain
26	chr2:56149400-56151400	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
27	chr2:56149400-56151400	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
28	chr2:56149400-56151400	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
29	chr2:56149400-56151400	Active TSS	HSMM	muscle
30	chr2:56149400-56151600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
31	chr2:56149600-56150600	Bivalent Enhancer	Fetal Brain Male	brain
32	chr2:56149600-56150800	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr2:56149600-56150800	Flanking Active TSS	Placenta	Placenta
34	chr2:56149600-56151000	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
35	chr2:56149600-56151200	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr2:56149600-56151200	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
37	chr2:56149600-56151200	Bivalent/Poised TSS	Thymus	Thymus
38	chr2:56149600-56151200	Active TSS	Hela-S3	cervix
39	chr2:56149600-56151200	Active TSS	HUVEC	blood vessel
40	chr2:56149600-56151200	Active TSS	NHLF	lung
41	chr2:56149600-56151400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
42	chr2:56149600-56151400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr2:56149600-56151400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
44	chr2:56149600-56151400	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr2:56149600-56151400	Active TSS	Breast Myoepithelial Primary Cells	Breast
46	chr2:56149600-56151400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr2:56149600-56151400	Bivalent/Poised TSS	Brain Angular Gyrus	brain
48	chr2:56149600-56151400	Bivalent/Poised TSS	Colonic Mucosa	Colon
49	chr2:56149600-56151400	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
50	chr2:56149600-56151400	Active TSS	Placenta Amnion	Placenta Amnion

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