Variant report

Variant	rs4676782
Chromosome Location	chr3:120145647-120145648
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:120143073..120145920-chr3:120273306..120275738,2	MCF-7	breast:
2	chr3:120145338..120147579-chr3:120153518..120155283,2	K562	blood:
3	chr3:120145331..120148802-chr3:120153199..120156349,3	K562	blood:
4	chr3:120144896..120146989-chr3:120150144..120153389,3	MCF-7	breast:

Extended variants
information (count: 59 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1056928	1.00[JPT][hapmap]
rs1147696	1.00[JPT][hapmap]
rs1147698	1.00[JPT][hapmap]
rs1147699	1.00[JPT][hapmap]
rs12173	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12192	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1259328	1.00[JPT][hapmap]
rs13061630	1.00[JPT][hapmap]
rs13066496	0.82[EUR][1000 genomes]
rs13070508	0.86[AMR][1000 genomes]
rs13081675	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13081694	0.96[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs13083670	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13088020	0.81[EUR][1000 genomes]
rs13096232	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13096256	0.92[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13096973	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13097755	0.96[CEU][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs13100865	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13709	1.00[JPT][hapmap]
rs1492272	1.00[JPT][hapmap]
rs1515577	1.00[JPT][hapmap]
rs17813772	0.84[CEU][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes]
rs1969356	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2030414	1.00[JPT][hapmap]
rs2091726	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2272515	0.96[CEU][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes]
rs2488	1.00[JPT][hapmap]
rs33935225	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34446218	0.88[EUR][1000 genomes]
rs34805176	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs36001904	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs36068602	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3755558	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4146299	1.00[JPT][hapmap]
rs4146300	1.00[JPT][hapmap]
rs4676696	0.83[AMR][1000 genomes]
rs4676698	0.92[CEU][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4676768	0.84[AMR][1000 genomes]
rs4676776	0.92[CEU][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4676777	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4676778	1.00[JPT][hapmap]
rs4676779	1.00[JPT][hapmap]
rs4676781	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4676783	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56100867	0.88[EUR][1000 genomes]
rs6438575	1.00[JPT][hapmap]
rs6775963	0.88[EUR][1000 genomes]
rs71327229	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs869247	1.00[JPT][hapmap]
rs9880550	1.00[JPT][hapmap]

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	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1007557	chr3:119892894-120764353	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv536706	chr3:119892894-120764353	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv1012127	chr3:120015620-120272893	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv536707	chr3:120015620-120272893	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv1006428	chr3:120015620-120421982	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	esv3369381	chr3:120066425-120425510	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	esv3350409	chr3:120066445-120425480	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4676782	RABL3	cis	cerebellum	SCAN
rs4676782	C3orf1	cis	cerebellum	SCAN
rs4676782	CD80	cis	cerebellum	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120115800-120151000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:120135400-120151600	Genic enhancers	Osteobl	bone
3	chr3:120136800-120147400	Enhancers	Duodenum Smooth Muscle	Duodenum
4	chr3:120136800-120147600	Enhancers	Adipose Nuclei	Adipose
5	chr3:120136800-120148400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr3:120136800-120148600	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr3:120137000-120149600	Enhancers	Rectal Smooth Muscle	rectum
8	chr3:120137400-120162200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr3:120137800-120161600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr3:120138200-120146400	Weak transcription	Fetal Intestine Large	intestine
11	chr3:120138200-120154200	Weak transcription	HMEC	breast
12	chr3:120138200-120157200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr3:120138200-120162000	Weak transcription	Primary hematopoietic stem cells	blood
14	chr3:120138200-120167800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr3:120138200-120169200	Weak transcription	Gastric	stomach
16	chr3:120138400-120148600	Genic enhancers	NHDF-Ad	bronchial
17	chr3:120138400-120155600	Weak transcription	Esophagus	oesophagus
18	chr3:120138600-120147800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr3:120138600-120148600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr3:120138800-120150600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr3:120139000-120148000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr3:120140800-120147600	Strong transcription	HSMM	muscle
23	chr3:120140800-120154200	Weak transcription	Psoas Muscle	Psoas
24	chr3:120141000-120145800	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr3:120141200-120147800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr3:120141200-120150800	Weak transcription	Brain Angular Gyrus	brain
27	chr3:120141400-120146600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr3:120142000-120146800	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr3:120142000-120148200	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr3:120142000-120148600	Enhancers	Aorta	Aorta
31	chr3:120142000-120149400	Genic enhancers	Fetal Stomach	stomach
32	chr3:120142000-120153600	Genic enhancers	NHLF	lung
33	chr3:120142400-120153600	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr3:120142600-120145800	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr3:120142600-120146000	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr3:120142600-120146800	Enhancers	Colon Smooth Muscle	Colon
37	chr3:120142600-120147600	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr3:120142600-120147600	Weak transcription	HUVEC	blood vessel
39	chr3:120142600-120147800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr3:120142800-120147200	Enhancers	Cortex derived primary cultured neurospheres	brain
41	chr3:120143000-120145800	Enhancers	Fetal Thymus	thymus
42	chr3:120143000-120147400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr3:120143200-120146200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr3:120143400-120146200	Enhancers	Fetal Lung	lung
45	chr3:120143600-120154200	Genic enhancers	NH-A	brain
46	chr3:120143800-120146000	Genic enhancers	HSMMtube	muscle
47	chr3:120143800-120149000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr3:120144200-120146000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr3:120144200-120146400	Enhancers	Fetal Kidney	kidney
50	chr3:120144200-120149200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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