Variant report

Variant	rs1350299
Chromosome Location	chr5:41414139-41414140
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	chr5:41284176..41286703-chr5:41413891..41416832,2	MCF-7	breast:

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10044440	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10053633	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10055126	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10068649	0.86[ASN][1000 genomes]
rs10071445	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10078334	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1037690	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.97[ASN][1000 genomes]
rs10805659	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13166710	0.90[ASN][1000 genomes]
rs1380996	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1460955	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs160966	0.90[ASN][1000 genomes]
rs161086	0.89[CHB][hapmap]
rs161087	0.85[ASN][1000 genomes]
rs1645060	1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs167627	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs167628	1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs223080	1.00[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs2925729	0.84[CHB][hapmap]
rs2925731	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs318836	1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs318837	1.00[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs318838	1.00[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs318839	0.85[ASN][1000 genomes]
rs318840	0.90[ASN][1000 genomes]
rs318841	1.00[CHB][hapmap];0.83[JPT][hapmap];0.88[ASN][1000 genomes]
rs318842	1.00[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs318843	1.00[CHB][hapmap];0.83[JPT][hapmap];0.90[ASN][1000 genomes]
rs318844	1.00[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs318845	1.00[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];0.90[ASN][1000 genomes]
rs318846	1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs318847	0.94[CHB][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs318849	0.85[ASN][1000 genomes]
rs319013	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs319014	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs319015	0.93[ASN][1000 genomes]
rs320622	0.83[ASN][1000 genomes]
rs320623	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs4051076	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4380706	0.86[ASN][1000 genomes]
rs4380707	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs4383755	0.86[ASN][1000 genomes]
rs4403222	1.00[CHB][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs4438921	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4557464	1.00[CHB][hapmap];0.83[JPT][hapmap];0.90[ASN][1000 genomes]
rs4559042	0.86[ASN][1000 genomes]
rs545358	0.86[ASN][1000 genomes]
rs6859578	1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs730354	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7700406	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7713441	0.89[ASN][1000 genomes]
rs7718012	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7722338	0.86[ASN][1000 genomes]
rs921946	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9292806	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];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9654393	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1851387	chr5:41336050-41423631	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
2	nsv1024631	chr5:41341979-41427953	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1350299	SEPP1	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:41409600-41414400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr5:41409600-41414400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr5:41409600-41414400	Weak transcription	HMEC	breast
4	chr5:41409600-41414400	Weak transcription	NH-A	brain
5	chr5:41409600-41414600	Weak transcription	HSMM	muscle
6	chr5:41409800-41414400	Weak transcription	Osteobl	bone
7	chr5:41409800-41418400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr5:41410000-41417800	Weak transcription	NHLF	lung
9	chr5:41411200-41416400	Weak transcription	Left Ventricle	heart
10	chr5:41412600-41414800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr5:41412600-41415600	Enhancers	NHDF-Ad	bronchial
12	chr5:41412800-41416600	Weak transcription	Right Atrium	heart
13	chr5:41412800-41416800	Enhancers	Hela-S3	cervix
14	chr5:41412800-41418400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr5:41413000-41419000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr5:41413200-41419400	Enhancers	Muscle Satellite Cultured Cells	--
17	chr5:41413400-41414600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr5:41413600-41414600	Enhancers	A549	lung
19	chr5:41413600-41415400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr5:41413600-41425400	Weak transcription	Ovary	ovary
21	chr5:41413800-41414600	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr5:41413800-41418200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr5:41414000-41414200	Enhancers	Placenta Amnion	Placenta Amnion
24	chr5:41414000-41414400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr5:41414000-41414400	Weak transcription	Fetal Heart	heart

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