Variant report

Variant	rs249005
Chromosome Location	chr5:79785691-79785692
allele	A/C
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	CEBPB	chr5:79785569-79785778	HepG2	liver:	n/a	n/a
2	CEBPB	chr5:79785556-79785827	H1-hESC	embryonic stem cell:	n/a	n/a
3	MAX	chr5:79785100-79786118	Hela-S3	cervix:	n/a	n/a
4	TCF7L2	chr5:79785183-79786118	HCT-116	colon:	n/a	n/a
5	CEBPB	chr5:79785427-79786044	HCT-116	colon:	n/a	n/a
6	TCF7L2	chr5:79785598-79786052	PANC-1	pancreas:	n/a	n/a
7	CEBPB	chr5:79785575-79785982	MCF-7	breast:	n/a	n/a
8	SMC3	chr5:79785383-79786170	Hela-S3	cervix:	n/a	n/a
9	MAFK	chr5:79785262-79785803	HepG2	liver:	n/a	chr5:79785420-79785436 chr5:79785421-79785432
10	POLR2A	chr5:79785294-79786192	Hela-S3	cervix:	n/a	n/a
11	HCFC1	chr5:79783161-79786211	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr5:79785305-79786147	Hela-S3	cervix:	n/a	n/a
13	CEBPB	chr5:79785535-79785846	K562	blood:	n/a	n/a
14	CEBPB	chr5:79785550-79785828	HepG2	liver:	n/a	n/a
15	CEBPB	chr5:79785368-79786228	HCT-116	colon:	n/a	n/a
16	MAFK	chr5:79785113-79786150	Hela-S3	cervix:	n/a	chr5:79785420-79785436 chr5:79785421-79785432
17	POLR2A	chr5:79783283-79786208	Hela-S3	cervix:	n/a	n/a
18	YY1	chr5:79785444-79785811	HepG2	liver:	n/a	n/a
19	CEBPD	chr5:79785527-79785802	HepG2	liver:	n/a	n/a
20	MAFF	chr5:79785258-79785803	HepG2	liver:	n/a	n/a
21	TBP	chr5:79783533-79786711	Hela-S3	cervix:	n/a	n/a
22	RCOR1	chr5:79785262-79785814	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr5:79785273-79785790	Hela-S3	cervix:	n/a	n/a
24	TCF7L2	chr5:79785145-79786220	Hela-S3	cervix:	n/a	n/a
25	MAFK	chr5:79785263-79785803	HepG2	liver:	n/a	chr5:79785420-79785436 chr5:79785421-79785432
26	POLR2A	chr5:79785252-79786189	Hela-S3	cervix:	n/a	n/a
27	CEBPB	chr5:79785566-79785961	MCF-7	breast:	n/a	n/a
28	CEBPB	chr5:79785549-79785846	K562	blood:	n/a	n/a
29	CEBPB	chr5:79785360-79786561	Hela-S3	cervix:	n/a	n/a
30	RFX5	chr5:79785166-79786258	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:79782822..79786705-chr5:79948261..79952248,11	MCF-7	breast:
2	chr5:79784731..79786261-chr5:79786333..79788295,2	MCF-7	breast:
3	chr5:79781713..79786255-chr5:79948613..79954295,12	MCF-7	breast:
4	chr5:79784119..79786030-chr5:79964336..79965848,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000249042	TF binding region
ENSG00000228716	Chromatin interaction
ENSG00000113318	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10433	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10942926	0.95[ASN][1000 genomes]
rs1097307	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1097308	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1097309	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1102116	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1103116	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1363775	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs168938	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs168939	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs171595	1.00[ASN][1000 genomes]
rs171596	1.00[ASN][1000 genomes]
rs173597	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs173598	0.82[ASN][1000 genomes]
rs173599	0.95[ASN][1000 genomes]
rs174075	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1820119	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs185100	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs187478	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs187479	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs192313	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs194540	0.83[ASN][1000 genomes]
rs2112152	0.81[EUR][1000 genomes]
rs2251759	0.95[ASN][1000 genomes]
rs248999	1.00[ASN][1000 genomes]
rs249000	0.88[ASN][1000 genomes]
rs249001	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249003	1.00[ASN][1000 genomes]
rs249004	1.00[ASN][1000 genomes]
rs249006	1.00[ASN][1000 genomes]
rs249016	0.92[ASN][1000 genomes]
rs249020	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs249021	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs249023	0.95[ASN][1000 genomes]
rs249024	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs249025	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs249026	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs249027	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs249028	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs249029	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249030	1.00[ASN][1000 genomes]
rs249031	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249032	1.00[ASN][1000 genomes]
rs249037	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249038	0.95[ASN][1000 genomes]
rs249039	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2544592	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2544593	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2544598	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2544599	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2544600	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2544603	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2544604	0.95[ASN][1000 genomes]
rs2547487	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs259023	0.85[ASN][1000 genomes]
rs259024	0.85[ASN][1000 genomes]
rs259025	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs259026	0.85[ASN][1000 genomes]
rs259027	0.85[ASN][1000 genomes]
rs259028	0.95[ASN][1000 genomes]
rs259029	0.95[ASN][1000 genomes]
rs259030	0.95[ASN][1000 genomes]
rs259031	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs259032	0.95[ASN][1000 genomes]
rs259033	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs259034	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs259041	0.81[EUR][1000 genomes]
rs259052	0.82[ASN][1000 genomes]
rs259055	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2599508	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3095851	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3096111	0.80[ASN][1000 genomes]
rs394076	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs394170	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs399261	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs401612	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs408899	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704674	0.95[ASN][1000 genomes]
rs557346	1.00[ASN][1000 genomes]
rs701380	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs835726	0.82[ASN][1000 genomes]
rs835729	0.87[ASN][1000 genomes]
rs856765	0.95[ASN][1000 genomes]
rs856772	1.00[ASN][1000 genomes]
rs863163	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs969567	0.86[EUR][1000 genomes];0.95[ASN][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	nsv948807	chr5:79549207-79805765	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv1028027	chr5:79694699-79841752	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79783200-79786000	Active TSS	Rectal Mucosa Donor 29	rectum
2	chr5:79783600-79786000	Active TSS	HepG2	liver
3	chr5:79783600-79786200	Active TSS	Duodenum Mucosa	Duodenum
4	chr5:79784600-79785800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr5:79784600-79785800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr5:79784600-79786000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr5:79784600-79787600	Weak transcription	Aorta	Aorta
8	chr5:79784600-79794600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr5:79784600-79797400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr5:79784800-79786200	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr5:79784800-79786600	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr5:79784800-79788800	Weak transcription	HMEC	breast
13	chr5:79784800-79806600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr5:79784800-79819400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr5:79785000-79787600	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr5:79785000-79788200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr5:79785000-79822800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr5:79785200-79788400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr5:79785200-79817600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr5:79785400-79786000	Active TSS	Colonic Mucosa	Colon
21	chr5:79785400-79786000	Active TSS	Placenta	Placenta
22	chr5:79785400-79786200	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr5:79785400-79786400	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr5:79785400-79786400	Active TSS	Hela-S3	cervix
25	chr5:79785400-79788400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr5:79785400-79788400	Weak transcription	NHEK	skin
27	chr5:79785400-79788600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr5:79785400-79788800	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr5:79785600-79786000	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr5:79785600-79786200	Enhancers	H1 Cell Line	embryonic stem cell
31	chr5:79785600-79786200	Enhancers	Sigmoid Colon	Sigmoid Colon

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