Variant report

Variant	rs3778370
Chromosome Location	chr6:167033291-167033292
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	chr6:167027450..167030161-chr6:167032275..167034525,2	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10946178	1.00[CEU][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12196315	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12199983	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12202785	0.83[JPT][hapmap]
rs12203904	1.00[CEU][hapmap];0.91[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.85[MEX][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12204787	1.00[CEU][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12215660	0.83[JPT][hapmap]
rs3778367	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3778369	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][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]
rs3778371	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3778372	1.00[CEU][hapmap];0.92[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3778373	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3778375	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3799566	0.81[ASW][hapmap];0.94[CEU][hapmap];0.88[MEX][hapmap];0.81[MKK][hapmap];0.82[EUR][1000 genomes]
rs3799570	0.94[CEU][hapmap];0.82[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3799571	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58727224	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60145177	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6456097	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs6456098	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs6916042	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6919949	0.83[JPT][hapmap]
rs6929319	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72503823	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs873070	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs873071	1.00[CEU][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs874153	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs916389	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs9356498	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs9364864	0.83[JPT][hapmap]
rs9366034	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs9459701	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3490076	chr6:166727901-167306743	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
2	esv3490077	chr6:166727901-167306743	Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
3	nsv605260	chr6:166984094-167455139	Enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
4	nsv432984	chr6:167018915-167181613	Bivalent Enhancer Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1023649	chr6:167026469-167060732	Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3778370	OSTN	trans	parietal	SCAN

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:167012400-167034400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:167016000-167034400	Weak transcription	Aorta	Aorta
3	chr6:167024000-167033600	Weak transcription	Fetal Brain Male	brain
4	chr6:167025400-167034800	Enhancers	Ovary	ovary
5	chr6:167025600-167034200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr6:167028200-167035400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr6:167028600-167034600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr6:167028800-167033400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr6:167028800-167033400	Weak transcription	Stomach Mucosa	stomach
10	chr6:167029200-167033400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr6:167029200-167034400	Weak transcription	Colonic Mucosa	Colon
12	chr6:167029200-167039000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr6:167029400-167036800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:167029600-167034200	Weak transcription	Brain Substantia Nigra	brain
15	chr6:167030200-167033800	Weak transcription	Brain Hippocampus Middle	brain
16	chr6:167030400-167033400	Weak transcription	Brain Cingulate Gyrus	brain
17	chr6:167030400-167033600	Weak transcription	Brain Anterior Caudate	brain
18	chr6:167030600-167033800	Weak transcription	Liver	Liver
19	chr6:167031400-167034400	Weak transcription	Fetal Kidney	kidney
20	chr6:167031600-167037200	Enhancers	Placenta Amnion	Placenta Amnion
21	chr6:167032200-167034600	Enhancers	HSMMtube	muscle
22	chr6:167032200-167034800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr6:167032200-167034800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
24	chr6:167032400-167033400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr6:167032400-167033400	Weak transcription	Fetal Intestine Large	intestine
26	chr6:167032400-167033800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr6:167032400-167033800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr6:167032400-167033800	Enhancers	Right Atrium	heart
29	chr6:167032400-167034200	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr6:167032400-167034400	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr6:167032400-167034400	Weak transcription	Spleen	Spleen
32	chr6:167032400-167035000	Enhancers	Fetal Heart	heart
33	chr6:167032600-167033400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr6:167032600-167033400	Weak transcription	Pancreas	Pancrea
35	chr6:167032600-167033800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr6:167032600-167033800	Enhancers	NHDF-Ad	bronchial
37	chr6:167032600-167034200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr6:167032600-167034200	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr6:167032600-167034200	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr6:167032600-167034200	Weak transcription	Duodenum Mucosa	Duodenum
41	chr6:167032600-167034200	Weak transcription	Gastric	stomach
42	chr6:167032600-167034400	Enhancers	HSMM	muscle
43	chr6:167032600-167034600	Enhancers	Esophagus	oesophagus
44	chr6:167032600-167034600	Enhancers	Right Ventricle	heart
45	chr6:167032600-167035200	Enhancers	Skeletal Muscle Male	skeletal muscle
46	chr6:167032600-167035400	Enhancers	Fetal Muscle Leg	muscle
47	chr6:167032600-167035400	Enhancers	Left Ventricle	heart
48	chr6:167032600-167035400	Enhancers	Skeletal Muscle Female	skeletal muscle
49	chr6:167032600-167035600	Enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr6:167032600-167035600	Enhancers	Brain Germinal Matrix	brain

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