Variant report

Variant	rs4380707
Chromosome Location	chr5:41405404-41405405
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	chr5:41404307..41406613-chr5:41408825..41411220,2	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	0.89[ASN][1000 genomes]
rs10053633	0.93[ASN][1000 genomes]
rs10055126	0.93[ASN][1000 genomes]
rs10068649	0.97[ASN][1000 genomes]
rs10071445	0.91[ASN][1000 genomes]
rs10078334	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs1037690	1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs10805659	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs13166710	0.87[ASN][1000 genomes]
rs1350299	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs1380996	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs1460955	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs160966	0.87[ASN][1000 genomes]
rs161086	0.89[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs161087	0.91[ASN][1000 genomes]
rs1645060	1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs167627	0.91[ASN][1000 genomes]
rs167628	1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs223080	1.00[CHB][hapmap];0.87[CHD][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs2925729	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs2925731	1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs318836	1.00[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs318837	1.00[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs318838	1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs318839	0.91[ASN][1000 genomes]
rs318840	0.87[ASN][1000 genomes]
rs318841	1.00[CHB][hapmap];0.82[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs318842	1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs318843	1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs318844	1.00[CHB][hapmap];0.91[JPT][hapmap];0.96[ASN][1000 genomes]
rs318845	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs318846	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs318847	0.94[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs318849	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs319013	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs319014	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs319015	0.95[ASN][1000 genomes]
rs320622	0.94[ASN][1000 genomes]
rs320623	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs4051076	0.93[ASN][1000 genomes]
rs4380706	0.97[ASN][1000 genomes]
rs4383755	0.97[ASN][1000 genomes]
rs4403222	1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs4438921	0.93[ASN][1000 genomes]
rs4557464	1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs4559042	0.81[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs545358	0.97[ASN][1000 genomes]
rs6859578	1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs730354	1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs7700406	1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs7713441	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7718012	0.93[ASN][1000 genomes]
rs7722338	0.97[ASN][1000 genomes]
rs921946	0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs9292806	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs9654393	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.89[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
rs4380707	C9	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:41389800-41409000	Weak transcription	Ovary	ovary
2	chr5:41392400-41409400	Weak transcription	Right Ventricle	heart
3	chr5:41392600-41408400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr5:41397600-41406600	Weak transcription	Left Ventricle	heart
5	chr5:41400800-41406200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr5:41402800-41406000	Enhancers	A549	lung
7	chr5:41404000-41412000	Enhancers	Fetal Heart	heart
8	chr5:41404400-41405800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr5:41404800-41407200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr5:41404800-41409800	Enhancers	Fetal Intestine Large	intestine
11	chr5:41405400-41405800	Weak transcription	Fetal Intestine Small	intestine
12	chr5:41405400-41410600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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