Variant report

Variant	rs880478
Chromosome Location	chr3:51377504-51377505
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:51376546..51378472-chr3:51379958..51381603,2	MCF-7	breast:
2	chr3:51373593..51375810-chr3:51376800..51379121,2	K562	blood:
3	chr3:51367010..51371078-chr3:51375773..51379297,4	MCF-7	breast:

Extended variants
information (count: 123 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs10510757	0.94[CHB][hapmap];0.89[JPT][hapmap];0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10510758	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12485610	0.84[ASN][1000 genomes]
rs12487426	0.84[ASN][1000 genomes]
rs12487468	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12489219	0.83[CHB][hapmap];0.80[AMR][1000 genomes]
rs12489414	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12490471	0.84[ASN][1000 genomes]
rs12490889	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12491048	0.92[ASN][1000 genomes]
rs12492615	0.89[CHB][hapmap]
rs12492624	0.84[ASN][1000 genomes]
rs12493034	0.84[AMR][1000 genomes]
rs12493265	0.83[ASN][1000 genomes]
rs12493323	0.88[CHB][hapmap];0.80[AMR][1000 genomes]
rs12493618	0.89[ASN][1000 genomes]
rs12493857	0.84[ASN][1000 genomes]
rs12493978	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12494462	0.84[ASN][1000 genomes]
rs12494979	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12495561	0.84[CHB][hapmap];0.84[AMR][1000 genomes]
rs13090348	0.89[ASN][1000 genomes]
rs1370124	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17051783	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17051799	0.89[YRI][hapmap]
rs17661242	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17712228	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1809388	0.84[AMR][1000 genomes]
rs1842394	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2033703	0.88[ASN][1000 genomes]
rs2082992	0.83[ASN][1000 genomes]
rs2082993	0.82[ASN][1000 genomes]
rs2086395	0.84[AMR][1000 genomes]
rs2101056	0.90[CHB][hapmap]
rs2127654	0.80[AMR][1000 genomes]
rs2170177	0.89[CHB][hapmap];0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2217938	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2241785	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2304512	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2306430	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2306431	1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2355946	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2356261	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2356298	0.84[ASN][1000 genomes]
rs3749317	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3762711	0.84[AMR][1000 genomes]
rs3792408	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3804766	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3828395	0.89[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4130473	0.90[CHB][hapmap]
rs4346580	0.83[CHB][hapmap]
rs4468966	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687553	0.82[ASN][1000 genomes]
rs4687563	0.82[ASN][1000 genomes]
rs4687601	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4687605	0.84[ASN][1000 genomes]
rs4687610	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4687656	0.83[ASN][1000 genomes]
rs4687691	0.81[ASN][1000 genomes]
rs4687731	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4687777	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4687794	0.81[ASN][1000 genomes]
rs4687811	0.89[ASN][1000 genomes]
rs4687812	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4687813	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4974096	1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4974098	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4974112	0.83[CHB][hapmap];0.84[AMR][1000 genomes]
rs55667499	0.82[ASN][1000 genomes]
rs56052360	0.84[AMR][1000 genomes]
rs56239081	0.84[ASN][1000 genomes]
rs56729479	0.84[ASN][1000 genomes]
rs57027950	0.89[ASN][1000 genomes]
rs57047724	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57603251	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57700326	0.81[AMR][1000 genomes]
rs57831708	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58059174	0.84[ASN][1000 genomes]
rs58201844	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58568178	0.87[ASN][1000 genomes]
rs58836277	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58911602	0.84[AMR][1000 genomes]
rs59129045	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs59563413	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59838596	0.83[ASN][1000 genomes]
rs59953568	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60128296	0.80[AMR][1000 genomes]
rs60567238	0.84[AMR][1000 genomes]
rs60606339	0.84[ASN][1000 genomes]
rs60740654	0.83[AMR][1000 genomes]
rs61233013	0.81[ASN][1000 genomes]
rs61419317	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61660900	0.84[AMR][1000 genomes]
rs61689323	0.83[ASN][1000 genomes]
rs72936442	0.83[AMR][1000 genomes]
rs72936462	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs72945708	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs72945713	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72951443	0.83[ASN][1000 genomes]
rs72953175	0.84[AMR][1000 genomes]
rs73834252	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73834253	0.86[ASN][1000 genomes]
rs73834254	0.86[ASN][1000 genomes]
rs73834258	0.84[ASN][1000 genomes]
rs73837439	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73837442	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73837443	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs751076	0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7642698	0.83[ASN][1000 genomes]
rs9817077	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9817872	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9819195	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9820140	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9829057	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9842600	0.81[ASN][1000 genomes]
rs9843583	0.81[ASN][1000 genomes]
rs9856134	1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9878592	0.83[CHB][hapmap];0.84[AMR][1000 genomes]
rs9880909	0.94[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005858	chr3:51090373-51444027	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv536569	chr3:51090373-51444027	Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv1014464	chr3:51220151-51909780	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS 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	53 gene(s)	inside rSNPs	diseases
4	esv20206	chr3:51344873-51415825	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51353400-51377600	Weak transcription	Left Ventricle	heart
2	chr3:51366400-51377600	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr3:51367600-51377800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:51369600-51383800	Weak transcription	Fetal Brain Male	brain
5	chr3:51372200-51377800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:51374800-51377600	Weak transcription	Colon Smooth Muscle	Colon
7	chr3:51375000-51377600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr3:51375000-51377800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr3:51375200-51377800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr3:51375400-51377600	Weak transcription	Fetal Muscle Leg	muscle
11	chr3:51375400-51377600	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr3:51375400-51378000	Strong transcription	Fetal Brain Female	brain
13	chr3:51375600-51377600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr3:51375600-51379000	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr3:51375800-51377600	Enhancers	Osteobl	bone
16	chr3:51376000-51377600	Weak transcription	Esophagus	oesophagus
17	chr3:51376200-51377600	Weak transcription	Gastric	stomach
18	chr3:51376400-51377600	Weak transcription	Right Ventricle	heart
19	chr3:51376400-51377600	Enhancers	Hela-S3	cervix
20	chr3:51376600-51377600	Weak transcription	Brain Substantia Nigra	brain
21	chr3:51376600-51377800	Weak transcription	Stomach Smooth Muscle	stomach
22	chr3:51376600-51378800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr3:51376600-51379400	Enhancers	NHLF	lung
24	chr3:51376800-51377600	Enhancers	Muscle Satellite Cultured Cells	--
25	chr3:51376800-51377600	Weak transcription	Brain Angular Gyrus	brain
26	chr3:51376800-51377600	Weak transcription	Brain Cingulate Gyrus	brain
27	chr3:51376800-51377600	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr3:51376800-51377800	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr3:51376800-51378400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr3:51376800-51378800	Enhancers	Aorta	Aorta
31	chr3:51376800-51379200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr3:51376800-51391800	Weak transcription	Brain Germinal Matrix	brain
33	chr3:51376800-51392400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr3:51377000-51377600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr3:51377000-51377600	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr3:51377000-51377600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr3:51377000-51377600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr3:51377000-51377600	Weak transcription	Brain Anterior Caudate	brain
39	chr3:51377000-51377600	Enhancers	HMEC	breast
40	chr3:51377000-51377600	Enhancers	NH-A	brain
41	chr3:51377000-51378000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr3:51377000-51378600	Enhancers	Adipose Nuclei	Adipose
43	chr3:51377000-51378600	Enhancers	Skeletal Muscle Male	skeletal muscle
44	chr3:51377000-51379400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr3:51377200-51377600	Enhancers	NHEK	skin
46	chr3:51377200-51377800	Enhancers	HUVEC	blood vessel
47	chr3:51377200-51378000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr3:51377200-51378000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr3:51377200-51378200	Weak transcription	Placenta	Placenta
50	chr3:51377200-51378600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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