Variant report

Variant	rs9867857
Chromosome Location	chr3:156491160-156491161
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	chr3:156489605..156491282-chr3:156493391..156495040,2	MCF-7	breast:
2	chr3:156483555..156485100-chr3:156490835..156492719,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SSR3-8	chr3:156490715-156491329	ucscGeneNc_uc003fah_1

Extended variants
information (count: 21 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12107178	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12492968	0.85[ASN][1000 genomes]
rs13061457	0.83[CHB][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs13068223	0.89[CHB][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs1430408	0.91[AFR][1000 genomes]
rs1469536	0.84[GIH][hapmap]
rs2043108	0.87[AFR][1000 genomes]
rs2054880	0.89[CHB][hapmap]
rs343994	0.89[CHB][hapmap]
rs3851992	0.84[ASW][hapmap];0.83[CHB][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];0.84[JPT][hapmap];0.87[LWK][hapmap];0.87[MEX][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs4098	1.00[ASW][hapmap];0.92[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];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4680317	0.84[ASW][hapmap]
rs7623691	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7638625	0.84[ASW][hapmap]
rs9818684	0.92[ASW][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs9818780	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9859058	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9878566	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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	nsv428745	chr3:156405054-156577840	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv877685	chr3:156444383-156611676	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
3	nsv877686	chr3:156489509-156557697	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs9867857	LINC00886	cis	Adipose Subcutaneous	GTEx
rs9867857	LINC00886	cis	Skin Sun Exposed Lower leg	GTEx
rs9867857	MUC7	trans	cerebellum	SCAN
rs9867857		cis	Lymphoblastoid	GTEx
rs9867857	SNORA5C	trans	cerebellum	SCAN
rs9867857	LINC00886	cis	Artery Tibial	GTEx
rs9867857	PPM1L	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156487600-156491200	Enhancers	NHEK	skin
2	chr3:156488400-156494400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr3:156488400-156494400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr3:156490200-156491400	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr3:156490200-156492200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr3:156490400-156491200	Enhancers	Muscle Satellite Cultured Cells	--
7	chr3:156490400-156491400	Enhancers	HMEC	breast
8	chr3:156490400-156491800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr3:156490600-156491200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr3:156490600-156491200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr3:156490600-156491200	Enhancers	Colon Smooth Muscle	Colon
12	chr3:156490600-156491200	Enhancers	NHDF-Ad	bronchial
13	chr3:156490600-156491200	Enhancers	Osteobl	bone
14	chr3:156490600-156491400	Enhancers	Brain Substantia Nigra	brain
15	chr3:156490600-156491600	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr3:156490600-156491600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr3:156490600-156491600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr3:156490600-156491600	Enhancers	Fetal Lung	lung
19	chr3:156490600-156491600	Enhancers	Fetal Stomach	stomach
20	chr3:156490800-156491200	Enhancers	A549	lung
21	chr3:156490800-156491400	Enhancers	Primary hematopoietic stem cells	blood
22	chr3:156490800-156491600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr3:156491000-156493800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr3:156491000-156494000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr3:156491000-156494000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr3:156491000-156494000	Weak transcription	HUVEC	blood vessel
27	chr3:156491000-156499200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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