Variant report

Variant	rs877681
Chromosome Location	chr3:46702573-46702574
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:46700787..46702922-chr3:46710281..46712322,2	K562	blood:
2	chr3:46701966..46703684-chr3:46705355..46706952,2	MCF-7	breast:
3	chr3:46702436..46704815-chr3:46735975..46737913,2	MCF-7	breast:
4	chr3:46670110..46673240-chr3:46702336..46706371,4	MCF-7	breast:
5	chr3:46700528..46705296-chr3:46732661..46735807,9	MCF-7	breast:
6	chr3:46697148..46699057-chr3:46702525..46705499,2	K562	blood:
7	chr3:46701509..46703825-chr3:47020121..47022596,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000178038	Chromatin interaction
ENSG00000160799	Chromatin interaction
ENSG00000160796	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11130102	0.83[JPT][hapmap]
rs11710586	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11719679	0.95[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs11922418	0.81[ASN][1000 genomes]
rs12491236	0.91[CHB][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12491294	0.91[CHB][hapmap];0.83[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13083665	0.81[ASN][1000 genomes]
rs1402148	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1520488	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1520489	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1581325	0.89[ASN][1000 genomes]
rs1607737	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34000414	0.89[ASN][1000 genomes]
rs34063921	0.88[ASN][1000 genomes]
rs34820891	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4234464	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4683256	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4683260	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4683271	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6442011	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6442012	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6774048	0.83[CEU][hapmap]
rs6808214	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7373994	0.89[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.82[YRI][hapmap];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7644072	0.88[EUR][1000 genomes]
rs877680	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs950190	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9845998	0.88[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	nsv1007449	chr3:46652343-46986578	Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv536554	chr3:46652343-46986578	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv876739	chr3:46656980-46744966	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv876740	chr3:46656980-46748453	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv876741	chr3:46663372-46763839	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	nsv516623	chr3:46680063-46852679	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	esv2757869	chr3:46680452-46972489	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
8	esv2759147	chr3:46680452-46972489	Genic enhancers Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46698000-46707600	Weak transcription	Gastric	stomach
2	chr3:46700400-46704200	Enhancers	iPS-20b Cell Line	embryonic stem cell
3	chr3:46700400-46704800	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr3:46700400-46705400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr3:46700400-46705800	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr3:46700400-46705800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr3:46700600-46702600	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr3:46700600-46703000	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr3:46700600-46703000	Enhancers	NHEK	skin
10	chr3:46700600-46704200	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr3:46700600-46705000	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr3:46700600-46705000	Enhancers	HMEC	breast
13	chr3:46700600-46705400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr3:46700600-46705600	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr3:46700800-46703000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr3:46700800-46704000	Enhancers	H1 Cell Line	embryonic stem cell
17	chr3:46700800-46705400	Enhancers	Placenta	Placenta
18	chr3:46700800-46710400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
19	chr3:46701000-46703000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:46701000-46704400	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr3:46701000-46704600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr3:46701000-46705000	Enhancers	H9 Cell Line	embryonic stem cell
23	chr3:46701200-46703600	Weak transcription	HSMMtube	muscle
24	chr3:46701200-46705400	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr3:46701400-46702600	Bivalent Enhancer	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr3:46701400-46702800	Enhancers	Adipose Nuclei	Adipose
27	chr3:46701400-46703000	Bivalent Enhancer	Fetal Muscle Leg	muscle
28	chr3:46701400-46703800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr3:46701400-46705200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr3:46701600-46702800	Enhancers	Pancreas	Pancrea
31	chr3:46701600-46702800	Enhancers	NHDF-Ad	bronchial
32	chr3:46701600-46703000	Enhancers	Esophagus	oesophagus
33	chr3:46701600-46703000	Enhancers	Left Ventricle	heart
34	chr3:46701600-46703600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
35	chr3:46701600-46706800	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr3:46701600-46709200	Enhancers	Right Ventricle	heart
37	chr3:46701800-46702800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr3:46701800-46702800	Enhancers	Right Atrium	heart
39	chr3:46702000-46702800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr3:46702000-46703200	Enhancers	Liver	Liver
41	chr3:46702000-46704400	Bivalent Enhancer	Fetal Stomach	stomach
42	chr3:46702200-46702600	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr3:46702200-46702600	Enhancers	Primary B cells from peripheral blood	blood
44	chr3:46702200-46702600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr3:46702200-46702600	Enhancers	Brain Anterior Caudate	brain
46	chr3:46702200-46702600	Bivalent Enhancer	Brain Cingulate Gyrus	brain
47	chr3:46702200-46702800	Enhancers	Brain Hippocampus Middle	brain
48	chr3:46702200-46702800	Enhancers	Psoas Muscle	Psoas
49	chr3:46702200-46703000	Enhancers	Lung	lung
50	chr3:46702200-46703000	Enhancers	Hela-S3	cervix

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