Variant report

Variant	rs4680748
Chromosome Location	chr3:28293360-28293361
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	CEBPB	chr3:28293170-28293583	HepG2	liver:	n/a	chr3:28293474-28293486 chr3:28293288-28293301 chr3:28293290-28293299 chr3:28293290-28293301 chr3:28293288-28293299 chr3:28293567-28293578 chr3:28293565-28293578
2	CEBPB	chr3:28293112-28293464	IMR90	lung:	n/a	chr3:28293288-28293301 chr3:28293290-28293299 chr3:28293290-28293301 chr3:28293288-28293299
3	CHD2	chr3:28293358-28293890	GM12878	blood:	n/a	n/a
4	EP300	chr3:28293344-28293988	GM12878	blood:	n/a	chr3:28293580-28293589 chr3:28293566-28293580
5	CEBPB	chr3:28293216-28293451	A549	lung:	n/a	chr3:28293288-28293301 chr3:28293290-28293299 chr3:28293290-28293301 chr3:28293288-28293299

No.	Distal block	Cell Line	Cell type
1	chr3:28282408..28284595-chr3:28291176..28293436,3	MCF-7	breast:
2	chr3:28291406..28295098-chr3:28302322..28306116,3	MCF-7	breast:
3	chr3:28291993..28293537-chr3:28308366..28309970,2	K562	blood:

Variant related genes	Relation type
CMC1	TF binding region
ENSG00000187118	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10510607	0.87[CHB][hapmap];0.83[CHD][hapmap]
rs10510609	0.87[CHB][hapmap]
rs12054402	0.82[CHB][hapmap]
rs12498078	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17021298	0.87[CHB][hapmap];0.83[CHD][hapmap]
rs4502545	0.87[CHB][hapmap]
rs4680906	0.87[CHB][hapmap]
rs60425255	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6800659	0.86[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6809706	0.87[LWK][hapmap];0.81[MKK][hapmap];0.81[YRI][hapmap]
rs6809917	0.85[YRI][hapmap]
rs6810242	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7633786	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9310864	0.87[CHB][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap]
rs9310865	0.86[CHB][hapmap]
rs966029	0.86[CHB][hapmap];0.86[JPT][hapmap]

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	esv3328565	chr3:27991169-28915035	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv876649	chr3:28126595-28718454	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:28283800-28311400	Weak transcription	Lung	lung
2	chr3:28284000-28304800	Weak transcription	Primary B cells from cord blood	blood
3	chr3:28284000-28309600	Weak transcription	Fetal Muscle Leg	muscle
4	chr3:28284000-28313800	Weak transcription	Ovary	ovary
5	chr3:28284000-28317200	Weak transcription	Gastric	stomach
6	chr3:28284400-28293600	Weak transcription	Right Ventricle	heart
7	chr3:28284400-28305400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr3:28284400-28305800	Weak transcription	Hela-S3	cervix
9	chr3:28284400-28311000	Weak transcription	Fetal Intestine Small	intestine
10	chr3:28284400-28312600	Weak transcription	Fetal Lung	lung
11	chr3:28284400-28321800	Weak transcription	NHLF	lung
12	chr3:28284600-28293400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr3:28284600-28305600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr3:28284600-28306000	Weak transcription	A549	lung
15	chr3:28284600-28307200	Weak transcription	Fetal Intestine Large	intestine
16	chr3:28284600-28311200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr3:28285200-28305200	Weak transcription	Primary hematopoietic stem cells	blood
18	chr3:28285200-28305600	Weak transcription	Fetal Thymus	thymus
19	chr3:28285400-28294000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr3:28285600-28315400	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr3:28285800-28305400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr3:28285800-28311000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr3:28286000-28294000	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr3:28286000-28306000	Weak transcription	K562	blood
25	chr3:28286000-28307200	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr3:28286200-28294400	Weak transcription	Spleen	Spleen
27	chr3:28287200-28304800	Weak transcription	Duodenum Mucosa	Duodenum
28	chr3:28287600-28317000	Weak transcription	Pancreas	Pancrea
29	chr3:28288200-28293600	Weak transcription	HepG2	liver
30	chr3:28288600-28293800	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr3:28288600-28305200	Weak transcription	Liver	Liver
32	chr3:28288600-28311200	Weak transcription	Esophagus	oesophagus
33	chr3:28289200-28293400	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr3:28289200-28293600	Weak transcription	Right Atrium	heart
35	chr3:28289400-28305200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr3:28289400-28305200	Weak transcription	Dnd41	blood
37	chr3:28290200-28293600	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr3:28291000-28293600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr3:28291000-28293600	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr3:28291000-28293600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr3:28291000-28293800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
42	chr3:28291000-28294000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr3:28291200-28293600	Enhancers	Primary T killer memory cells from peripheral blood	blood
44	chr3:28291200-28295800	Enhancers	Primary monocytes fromperipheralblood	blood
45	chr3:28291400-28293600	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr3:28291400-28311200	Weak transcription	Aorta	Aorta
47	chr3:28292000-28295600	Enhancers	Primary T helper cells fromperipheralblood	blood
48	chr3:28292200-28293400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
49	chr3:28292200-28293800	Enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr3:28292200-28294000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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