Variant report

Variant	rs10167115
Chromosome Location	chr2:56150849-56150850
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	E2F6	chr2:56150261-56151205	H1-hESC	embryonic stem cell:	n/a	chr2:56150780-56150792 chr2:56151077-56151086 chr2:56151106-56151116 chr2:56151102-56151114
2	POLR2A	chr2:56150766-56150893	Hela-S3	cervix:	n/a	n/a
3	CTCF	chr2:56150840-56150990	WERI-Rb-1	eye:	n/a	n/a
4	RAD21	chr2:56150642-56151117	H1-hESC	embryonic stem cell:	n/a	chr2:56151079-56151089
5	E2F6	chr2:56150461-56151191	H1-hESC	embryonic stem cell:	n/a	chr2:56150780-56150792 chr2:56151077-56151086 chr2:56151106-56151116 chr2:56151102-56151114
6	MXI1	chr2:56149060-56151667	IMR90	lung:	n/a	n/a
7	GATA3	chr2:56150466-56151059	T-47D	breast:	n/a	n/a
8	POLR2A	chr2:56150609-56151121	Gliobla	brain:	n/a	n/a
9	MAZ	chr2:56150309-56151220	Hela-S3	cervix:	n/a	chr2:56151182-56151193
10	REST	chr2:56150745-56151046	SK-N-SH	brain:	n/a	n/a
11	E2F6	chr2:56150318-56151274	A549	lung:	n/a	chr2:56150780-56150792 chr2:56151077-56151086 chr2:56151106-56151116 chr2:56151102-56151114
12	TEAD4	chr2:56150439-56150927	ECC-1	luminal epithelium:	n/a	n/a
13	E2F6	chr2:56150741-56151328	A549	lung:	n/a	chr2:56150780-56150792 chr2:56151077-56151086 chr2:56151106-56151116 chr2:56151102-56151114
14	POLR2A	chr2:56150230-56150970	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr2:56150388-56151034	MCF10A-Er-Src	breast:	n/a	n/a
16	RAD21	chr2:56150458-56151153	MCF-7	breast:	n/a	chr2:56151079-56151089
17	SMC3	chr2:56150325-56151245	Hela-S3	cervix:	n/a	chr2:56151079-56151089
18	POLR2A	chr2:56149657-56151154	MCF10A-Er-Src	breast:	n/a	n/a
19	EP300	chr2:56150321-56151384	SK-N-SH	brain:	n/a	n/a
20	MXI1	chr2:56150422-56150915	H1-hESC	embryonic stem cell:	n/a	n/a
21	CTBP2	chr2:56150129-56151225	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr2:56150782-56150960	A549	lung:	n/a	n/a
23	TCF12	chr2:56150371-56151103	A549	lung:	n/a	chr2:56150532-56150539
24	MAX	chr2:56150538-56150926	A549	lung:	n/a	n/a
25	SIN3AK20	chr2:56150399-56151097	SK-N-SH	brain:	n/a	n/a
26	HDAC2	chr2:56150561-56150945	H1-hESC	embryonic stem cell:	n/a	n/a
27	MAX	chr2:56150402-56151434	A549	lung:	n/a	chr2:56151182-56151193
28	TBP	chr2:56150321-56151350	H1-hESC	embryonic stem cell:	n/a	n/a
29	RAD21	chr2:56150455-56150849	Hela-S3	cervix:	n/a	n/a
30	TEAD4	chr2:56150283-56151351	SK-N-SH	brain:	n/a	n/a
31	SIN3AK20	chr2:56150720-56151216	PFSK-1	brain:	n/a	n/a
32	CTCF	chr2:56150601-56151119	IMR90	lung:	n/a	chr2:56151080-56151090 chr2:56151079-56151092
33	MAX	chr2:56150347-56151381	SK-N-SH	brain:	n/a	chr2:56151182-56151193
34	MYC	chr2:56150297-56150922	MCF10A-Er-Src	breast:	n/a	n/a
35	CHD2	chr2:56150501-56151164	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr2:56150777-56151176	SK-N-SH	brain:	n/a	n/a
37	MXI1	chr2:56150053-56150850	Hela-S3	cervix:	n/a	n/a
38	MAX	chr2:56149561-56151225	H1-hESC	embryonic stem cell:	n/a	chr2:56151182-56151193
39	E2F6	chr2:56150848-56151055	K562	blood:	n/a	n/a
40	TEAD4	chr2:56150395-56151205	H1-hESC	embryonic stem cell:	n/a	n/a
41	POLR2A	chr2:56150377-56151150	MCF-7	breast:	n/a	n/a
42	MAX	chr2:56150242-56151278	H1-hESC	embryonic stem cell:	n/a	chr2:56151182-56151193
43	TAF1	chr2:56150695-56151101	H1-hESC	embryonic stem cell:	n/a	n/a
44	CTCF	chr2:56150820-56151110	Hela-S3	cervix:	n/a	chr2:56151080-56151090 chr2:56151079-56151092
45	POLR2A	chr2:56150454-56151001	H1-hESC	embryonic stem cell:	n/a	n/a
46	YY1	chr2:56150403-56150875	H1-hESC	embryonic stem cell:	n/a	n/a
47	ZBTB7A	chr2:56150698-56151294	ECC-1	luminal epithelium:	n/a	chr2:56151078-56151087
48	SIN3A	chr2:56149537-56151428	H1-hESC	embryonic stem cell:	n/a	chr2:56150484-56150493
49	POLR2A	chr2:56146785-56151297	HUVEC	blood vessel:	n/a	n/a
50	RAD21	chr2:56150609-56151113	H1-hESC	embryonic stem cell:	n/a	chr2:56151079-56151089

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PNPT1-3	chr2:56150846-56150917	NONHSAT070808
2	lnc-PNPT1-3	chr2:56150846-56150932	NONHSAT070807

Variant related genes	Relation type
EFEMP1	TF binding region

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10201208	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10469935	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13429887	0.95[EUR][1000 genomes]
rs14282	0.95[EUR][1000 genomes]
rs28370328	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28371015	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55886642	0.95[EUR][1000 genomes]
rs56210563	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56268747	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6707184	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6718023	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6736923	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6737397	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6748550	0.90[EUR][1000 genomes]
rs72811703	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72811704	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72811714	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72811719	0.95[EUR][1000 genomes]
rs7562440	1.00[AMR][1000 genomes];0.95[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:100 , 50 per page) page: 1 2

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	chr2:56149400-56151000	Bivalent/Poised TSS	Left Ventricle	heart
18	chr2:56149400-56151000	Active TSS	Lung	lung
19	chr2:56149400-56151200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
20	chr2:56149400-56151200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr2:56149400-56151400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:56149400-56151400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr2:56149400-56151400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
24	chr2:56149400-56151400	Active TSS	Brain Substantia Nigra	brain
25	chr2:56149400-56151400	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
26	chr2:56149400-56151400	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
27	chr2:56149400-56151400	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
28	chr2:56149400-56151400	Active TSS	HSMM	muscle
29	chr2:56149400-56151600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
30	chr2:56149600-56151000	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
31	chr2:56149600-56151200	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr2:56149600-56151200	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
33	chr2:56149600-56151200	Bivalent/Poised TSS	Thymus	Thymus
34	chr2:56149600-56151200	Active TSS	Hela-S3	cervix
35	chr2:56149600-56151200	Active TSS	HUVEC	blood vessel
36	chr2:56149600-56151200	Active TSS	NHLF	lung
37	chr2:56149600-56151400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
38	chr2:56149600-56151400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr2:56149600-56151400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
40	chr2:56149600-56151400	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr2:56149600-56151400	Active TSS	Breast Myoepithelial Primary Cells	Breast
42	chr2:56149600-56151400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr2:56149600-56151400	Bivalent/Poised TSS	Brain Angular Gyrus	brain
44	chr2:56149600-56151400	Bivalent/Poised TSS	Colonic Mucosa	Colon
45	chr2:56149600-56151400	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
46	chr2:56149600-56151400	Active TSS	Placenta Amnion	Placenta Amnion
47	chr2:56149600-56151400	Active TSS	Rectal Smooth Muscle	rectum
48	chr2:56149600-56151400	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
49	chr2:56149600-56151600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
50	chr2:56149800-56151200	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland

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