Variant report

Variant	rs2043662
Chromosome Location	chr3:78733282-78733283
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:78731540..78733318-chr3:78736558..78739204,2	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10865570	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11708898	0.83[AFR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11714414	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11927671	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs2118067	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2164549	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2255164	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2608023	1.00[CEU][hapmap];0.95[YRI][hapmap];0.87[EUR][1000 genomes]
rs2684377	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28429251	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4681009	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6769521	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6785152	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7619742	0.80[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7631285	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs967454	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9834909	0.83[AFR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9837496	1.00[CEU][hapmap];0.84[TSI][hapmap];0.81[YRI][hapmap];0.86[EUR][1000 genomes]
rs984138	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9842948	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9856624	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9864412	0.96[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9875094	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529995	chr3:78188643-78739698	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv1008156	chr3:78444137-78765884	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	esv3413182	chr3:78730462-78737760	Weak transcription Strong transcription ZNF genes & repeats Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:78654200-78746600	Weak transcription	NHDF-Ad	bronchial
2	chr3:78667200-78751200	Weak transcription	Esophagus	oesophagus
3	chr3:78679400-78736600	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr3:78703200-78739200	Weak transcription	Fetal Muscle Trunk	muscle
5	chr3:78706400-78736200	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr3:78706600-78735200	Weak transcription	Primary T cells from cord blood	blood
7	chr3:78706600-78736400	Weak transcription	Stomach Smooth Muscle	stomach
8	chr3:78707000-78735400	Weak transcription	Rectal Smooth Muscle	rectum
9	chr3:78716000-78739600	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr3:78717600-78739600	Weak transcription	Osteobl	bone
11	chr3:78717800-78736800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr3:78717800-78745200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr3:78717800-78748400	Weak transcription	Ovary	ovary
14	chr3:78718600-78739200	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr3:78719400-78736800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr3:78719600-78753000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr3:78720000-78737800	Weak transcription	Fetal Brain Female	brain
18	chr3:78720000-78753200	Weak transcription	Brain Hippocampus Middle	brain
19	chr3:78724400-78738200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr3:78724800-78733400	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr3:78727200-78738200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr3:78730400-78752600	Weak transcription	Fetal Stomach	stomach
23	chr3:78730800-78738600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr3:78731000-78733600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr3:78731200-78736600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr3:78731200-78737800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr3:78731400-78738600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr3:78731600-78739800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr3:78732800-78735600	Weak transcription	Placenta	Placenta
30	chr3:78732800-78736200	Weak transcription	HepG2	liver
31	chr3:78733000-78735000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr3:78733200-78733800	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr3:78733200-78733800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr3:78733200-78733800	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr3:78733200-78733800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr3:78733200-78733800	Strong transcription	Fetal Kidney	kidney
37	chr3:78733200-78733800	Strong transcription	Fetal Lung	lung
38	chr3:78733200-78734000	Strong transcription	Duodenum Smooth Muscle	Duodenum
39	chr3:78733200-78734200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr3:78733200-78735000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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