Variant report

Variant	rs7621889
Chromosome Location	chr3:158048770-158048771
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	chr3:158048483..158050951-chr3:158053605..158056393,2	MCF-7	breast:
2	chr3:158046999..158049118-chr3:158139180..158140749,2	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1070894	0.83[ASN][1000 genomes]
rs1095629	0.85[ASN][1000 genomes]
rs1095630	0.81[ASN][1000 genomes]
rs1095633	0.82[ASN][1000 genomes]
rs1095634	0.83[ASN][1000 genomes]
rs11707696	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11719388	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1210358	0.97[ASN][1000 genomes]
rs1724676	0.86[ASN][1000 genomes]
rs1724677	0.86[ASN][1000 genomes]
rs1730054	0.86[ASN][1000 genomes]
rs2693528	0.96[ASN][1000 genomes]
rs2693541	0.95[ASN][1000 genomes]
rs57361244	0.86[ASN][1000 genomes]
rs698990	0.86[ASN][1000 genomes]
rs698991	0.86[ASN][1000 genomes]
rs699916	0.82[ASN][1000 genomes]
rs699917	0.82[ASN][1000 genomes]
rs699919	0.82[ASN][1000 genomes]
rs73168795	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7614091	0.87[ASN][1000 genomes]
rs7617666	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs827090	0.88[ASN][1000 genomes]
rs827091	0.86[ASN][1000 genomes]
rs827118	0.97[ASN][1000 genomes]
rs827120	0.97[ASN][1000 genomes]
rs827122	0.86[ASN][1000 genomes]
rs827123	0.86[ASN][1000 genomes]
rs827125	0.86[ASN][1000 genomes]
rs827136	0.93[ASN][1000 genomes]
rs827172	0.82[ASN][1000 genomes]
rs827175	0.81[ASN][1000 genomes]
rs827187	0.99[ASN][1000 genomes]
rs827188	0.99[ASN][1000 genomes]
rs9814827	0.87[ASN][1000 genomes]
rs9845388	0.84[AMR][1000 genomes];0.96[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	nsv1013391	chr3:157505943-158115553	Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv536775	chr3:157505943-158115553	Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1002378	chr3:157715428-158673414	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv877689	chr3:157858930-158133307	Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv916910	chr3:157926799-158183372	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7621889	RP11-538P18.2	cis	Adipose Subcutaneous	GTEx
rs7621889	RP11-538P18.2	cis	Skin Sun Exposed Lower leg	GTEx
rs7621889	RSRC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:157993400-158054600	Weak transcription	Primary T cells from cord blood	blood
2	chr3:158047000-158055400	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr3:158047800-158048800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:158047800-158064800	Weak transcription	Ovary	ovary
5	chr3:158047800-158077800	Weak transcription	Gastric	stomach
6	chr3:158048000-158054000	Weak transcription	Left Ventricle	heart
7	chr3:158048000-158056400	Weak transcription	Esophagus	oesophagus
8	chr3:158048000-158059800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr3:158048200-158049000	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr3:158048200-158049000	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr3:158048200-158049000	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr3:158048200-158049000	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr3:158048200-158053800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr3:158048200-158079400	Weak transcription	Right Ventricle	heart
15	chr3:158048400-158049200	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr3:158048600-158049000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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