Variant report

Variant	rs528551
Chromosome Location	chr2:31607545-31607546
allele	C/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	TEAD4	chr2:31607523-31608169	A549	lung:	n/a	n/a
2	BRCA1	chr2:31607458-31608012	Hela-S3	cervix:	n/a	n/a
3	BCL3	chr2:31607173-31608244	A549	lung:	n/a	chr2:31607409-31607418
4	POLR2A	chr2:31607137-31607946	Hela-S3	cervix:	n/a	n/a
5	GTF2F1	chr2:31607213-31608361	Hela-S3	cervix:	n/a	n/a
6	RAD21	chr2:31607418-31607944	A549	lung:	n/a	n/a
7	NFIC	chr2:31606973-31608549	SK-N-SH	brain:	n/a	n/a
8	MAX	chr2:31607236-31608160	Hela-S3	cervix:	n/a	chr2:31607409-31607418
9	MAX	chr2:31607113-31607604	SK-N-SH	brain:	n/a	chr2:31607409-31607418
10	NR3C1	chr2:31607526-31608128	A549	lung:	n/a	n/a
11	JUND	chr2:31607136-31608100	HCT-116	colon:	n/a	chr2:31607408-31607420 chr2:31607410-31607418
12	SP1	chr2:31607117-31608178	HCT-116	colon:	n/a	chr2:31607543-31607557 chr2:31607659-31607666
13	CBX3	chr2:31607095-31608068	HCT-116	colon:	n/a	n/a
14	SMC3	chr2:31607245-31608288	Hela-S3	cervix:	n/a	n/a
15	RXRA	chr2:31607089-31608160	SK-N-SH	brain:	n/a	n/a
16	FOS	chr2:31606726-31608111	MCF10A-Er-Src	breast:	n/a	chr2:31607408-31607420 chr2:31607408-31607419 chr2:31607410-31607418
17	FOS	chr2:31607226-31608122	MCF10A-Er-Src	breast:	n/a	chr2:31607408-31607420 chr2:31607408-31607419 chr2:31607410-31607418
18	NFIC	chr2:31607149-31608077	SK-N-SH	brain:	n/a	n/a
19	STAT3	chr2:31607272-31608110	MCF10A-Er-Src	breast:	n/a	chr2:31607540-31607552
20	STAT3	chr2:31606697-31608190	MCF10A-Er-Src	breast:	n/a	chr2:31607540-31607552
21	EP300	chr2:31607149-31608221	A549	lung:	n/a	n/a
22	MYC	chr2:31607296-31608272	MCF10A-Er-Src	breast:	n/a	chr2:31607409-31607418
23	JUND	chr2:31606800-31608429	SK-N-SH	brain:	n/a	chr2:31607408-31607420 chr2:31607410-31607418
24	PBX3	chr2:31607130-31608148	SK-N-SH	brain:	n/a	n/a
25	CEBPB	chr2:31607119-31608244	HCT-116	colon:	n/a	n/a
26	FOSL2	chr2:31607072-31608252	SK-N-SH	brain:	n/a	chr2:31607408-31607420 chr2:31607410-31607418
27	POLR2A	chr2:31606473-31608097	MCF10A-Er-Src	breast:	n/a	n/a
28	POLR2A	chr2:31607172-31608013	Hela-S3	cervix:	n/a	n/a
29	MYC	chr2:31607224-31608097	MCF10A-Er-Src	breast:	n/a	chr2:31607409-31607418
30	RAD21	chr2:31607206-31608180	Hela-S3	cervix:	n/a	n/a
31	GATA3	chr2:31607023-31608210	SK-N-SH	brain:	n/a	chr2:31607819-31607829
32	POLR2A	chr2:31607146-31608021	SK-N-SH	brain:	n/a	n/a
33	SP1	chr2:31607101-31608281	A549	lung:	n/a	chr2:31607543-31607557 chr2:31607659-31607666
34	FOSL2	chr2:31607121-31608383	A549	lung:	n/a	chr2:31607408-31607420 chr2:31607410-31607418
35	EP300	chr2:31607215-31607824	SK-N-SH_RA	brain:	n/a	n/a
36	FOS	chr2:31607207-31608308	MCF10A-Er-Src	breast:	n/a	chr2:31607408-31607420 chr2:31607408-31607419 chr2:31607410-31607418
37	STAT3	chr2:31607468-31608104	MCF10A-Er-Src	breast:	n/a	chr2:31607540-31607552
38	TCF12	chr2:31606488-31608278	SK-N-SH	brain:	n/a	n/a
39	MAX	chr2:31607114-31607612	SK-N-SH	brain:	n/a	chr2:31607409-31607418
40	E2F4	chr2:31607168-31607991	MCF10A-Er-Src	breast:	n/a	n/a
41	TFAP2C	chr2:31607385-31608270	Hela-S3	cervix:	n/a	n/a
42	POLR2A	chr2:31607177-31608071	Hela-S3	cervix:	n/a	n/a
43	GATA3	chr2:31607071-31608347	A549	lung:	n/a	chr2:31607819-31607829
44	ATF3	chr2:31607258-31608244	A549	lung:	n/a	n/a
45	CEBPB	chr2:31607277-31608248	IMR90	lung:	n/a	n/a
46	RFX5	chr2:31607354-31608150	Hela-S3	cervix:	n/a	n/a
47	JUND	chr2:31607050-31608169	Hela-S3	cervix:	n/a	chr2:31607408-31607420 chr2:31607410-31607418
48	CEBPB	chr2:31607119-31608313	A549	lung:	n/a	n/a
49	MEF2A	chr2:31607271-31608134	SK-N-SH	brain:	n/a	chr2:31607410-31607418
50	TCF12	chr2:31607523-31608110	A549	lung:	n/a	n/a

Variant related genes	Relation type
XDH	TF binding region

Extended variants
information (count: 19 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12712316	0.85[ASN][1000 genomes]
rs206797	1.00[CEU][hapmap]
rs206799	1.00[CEU][hapmap]
rs206810	1.00[CEU][hapmap]
rs206850	0.82[EUR][1000 genomes]
rs206856	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs206857	1.00[JPT][hapmap]
rs473935	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs513311	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs561525	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs71444496	0.92[EUR][1000 genomes];0.85[ASN][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	nsv949028	chr2:31502801-31665108	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
2	esv2762446	chr2:31521093-31610311	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv532648	chr2:31591498-32312698	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
4	nsv456030	chr2:31598823-31820256	Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv456041	chr2:31598823-31820256	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv581269	chr2:31598823-31820256	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv998853	chr2:31601455-31858961	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1005565	chr2:31603134-31868877	Genic enhancers Active TSS Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:31548000-31634600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr2:31565200-31633000	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr2:31574600-31636600	Weak transcription	Colonic Mucosa	Colon
4	chr2:31586000-31613000	Weak transcription	Small Intestine	intestine
5	chr2:31598400-31639000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr2:31599600-31636600	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr2:31600600-31608000	Weak transcription	Esophagus	oesophagus
8	chr2:31602200-31613400	Strong transcription	Duodenum Mucosa	Duodenum
9	chr2:31602800-31614200	Strong transcription	Liver	Liver
10	chr2:31603000-31612000	Strong transcription	Fetal Intestine Large	intestine
11	chr2:31603000-31612400	Strong transcription	Fetal Intestine Small	intestine
12	chr2:31604200-31609400	Enhancers	Placenta	Placenta
13	chr2:31604600-31608000	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr2:31604600-31608600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr2:31604600-31609800	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr2:31605200-31607600	Weak transcription	Stomach Mucosa	stomach
17	chr2:31605200-31608600	Enhancers	NH-A	brain
18	chr2:31605200-31608800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr2:31605200-31609000	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr2:31605200-31609600	Genic enhancers	HMEC	breast
21	chr2:31605200-31612600	Genic enhancers	NHEK	skin
22	chr2:31605400-31608400	Enhancers	HSMM	muscle
23	chr2:31605400-31608600	Enhancers	NHLF	lung
24	chr2:31605400-31609600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr2:31605600-31608400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr2:31605600-31608600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr2:31605600-31608800	Enhancers	NHDF-Ad	bronchial
28	chr2:31605800-31608400	Enhancers	HSMMtube	muscle
29	chr2:31605800-31608600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr2:31606000-31608000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
31	chr2:31606200-31609200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr2:31606200-31610600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr2:31606400-31607800	Flanking Active TSS	A549	lung
34	chr2:31606400-31607800	Flanking Active TSS	Hela-S3	cervix
35	chr2:31606400-31608400	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr2:31606600-31607800	Enhancers	GM12878-XiMat	blood
37	chr2:31606600-31608200	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr2:31606600-31612600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr2:31606800-31607600	Enhancers	HUES64 Cell Line	embryonic stem cell
40	chr2:31606800-31607800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr2:31606800-31607800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr2:31607000-31608000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr2:31607000-31608000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr2:31607200-31607600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr2:31607200-31607800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr2:31607200-31608000	Enhancers	ES-I3 Cell Line	embryonic stem cell
47	chr2:31607400-31607800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr2:31607400-31607800	Enhancers	Primary hematopoietic stem cells	blood
49	chr2:31607400-31607800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr2:31607400-31607800	Flanking Active TSS	Osteobl	bone

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