Variant report

Variant	rs4676781
Chromosome Location	chr3:120142951-120142952
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:120142587..120145112-chr3:120167743..120170457,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163430	Chromatin interaction

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[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12192	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1259328	1.00[JPT][hapmap]
rs13061630	1.00[JPT][hapmap]
rs13066496	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13070508	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13081675	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13081694	0.96[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs13083670	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13088020	0.83[EUR][1000 genomes]
rs13096232	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13096256	0.92[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13096973	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13097755	0.96[CEU][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes]
rs13100865	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[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];0.82[MEX][hapmap];0.87[TSI][hapmap];0.88[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2272515	0.96[CEU][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes]
rs2488	1.00[JPT][hapmap]
rs33935225	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34446218	0.90[EUR][1000 genomes]
rs34805176	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs36001904	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs36068602	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3755558	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4146299	1.00[JPT][hapmap]
rs4146300	1.00[JPT][hapmap]
rs4676696	0.88[AMR][1000 genomes]
rs4676698	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];0.90[TSI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4676768	0.90[AMR][1000 genomes]
rs4676776	0.82[ASW][hapmap];0.92[CEU][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4676777	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4676778	1.00[JPT][hapmap]
rs4676779	1.00[JPT][hapmap]
rs4676782	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];0.88[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56100867	0.90[EUR][1000 genomes]
rs6438575	1.00[ASW][hapmap];1.00[JPT][hapmap];0.94[MKK][hapmap]
rs6775963	0.90[EUR][1000 genomes]
rs71327229	0.89[AMR][1000 genomes];0.82[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
rs4676781	RABL3	cis	cerebellum	SCAN
rs4676781	C3orf1	cis	cerebellum	SCAN
rs4676781	CD80	cis	cerebellum	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120114400-120143200	Weak transcription	Small Intestine	intestine
2	chr3:120115800-120151000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:120135400-120151600	Genic enhancers	Osteobl	bone
4	chr3:120136800-120145200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr3:120136800-120147400	Enhancers	Duodenum Smooth Muscle	Duodenum
6	chr3:120136800-120147600	Enhancers	Adipose Nuclei	Adipose
7	chr3:120136800-120148400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr3:120136800-120148600	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr3:120137000-120149600	Enhancers	Rectal Smooth Muscle	rectum
10	chr3:120137400-120162200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr3:120137800-120161600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr3:120138200-120145400	Weak transcription	NHEK	skin
13	chr3:120138200-120146400	Weak transcription	Fetal Intestine Large	intestine
14	chr3:120138200-120154200	Weak transcription	HMEC	breast
15	chr3:120138200-120157200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr3:120138200-120162000	Weak transcription	Primary hematopoietic stem cells	blood
17	chr3:120138200-120167800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr3:120138200-120169200	Weak transcription	Gastric	stomach
19	chr3:120138400-120143000	Weak transcription	Fetal Thymus	thymus
20	chr3:120138400-120148600	Genic enhancers	NHDF-Ad	bronchial
21	chr3:120138400-120155600	Weak transcription	Esophagus	oesophagus
22	chr3:120138600-120147800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr3:120138600-120148600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr3:120138800-120150600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr3:120139000-120148000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr3:120139200-120145000	Weak transcription	Liver	Liver
27	chr3:120139400-120143200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr3:120139800-120144000	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr3:120140200-120143600	Enhancers	Right Ventricle	heart
30	chr3:120140600-120143400	Weak transcription	Ovary	ovary
31	chr3:120140600-120143600	Weak transcription	Pancreas	Pancrea
32	chr3:120140600-120143600	Weak transcription	Spleen	Spleen
33	chr3:120140600-120145000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr3:120140800-120144200	Weak transcription	Fetal Intestine Small	intestine
35	chr3:120140800-120145000	Weak transcription	Brain Substantia Nigra	brain
36	chr3:120140800-120147600	Strong transcription	HSMM	muscle
37	chr3:120140800-120154200	Weak transcription	Psoas Muscle	Psoas
38	chr3:120141000-120144200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr3:120141000-120144200	Weak transcription	Fetal Kidney	kidney
40	chr3:120141000-120144400	Strong transcription	Muscle Satellite Cultured Cells	--
41	chr3:120141000-120145800	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr3:120141200-120143200	Weak transcription	Brain Hippocampus Middle	brain
43	chr3:120141200-120145400	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr3:120141200-120147800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr3:120141200-120150800	Weak transcription	Brain Angular Gyrus	brain
46	chr3:120141400-120146600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr3:120141600-120143800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr3:120141600-120145200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr3:120142000-120143000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr3:120142000-120143200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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