Variant report

Variant	rs7310408
Chromosome Location	chr12:47077385-47077386
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr12:47076925-47077449	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:46776440..46778340-chr12:47077139..47078677,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000271642	TF binding region
ENSG00000257261	Chromatin interaction

Extended variants
information (count: 124 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:118)

rs_ID	r²[population]
rs11183524	0.88[EUR][1000 genomes]
rs11183536	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11183539	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11183547	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11183550	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11830099	0.83[EUR][1000 genomes]
rs11830501	0.83[EUR][1000 genomes]
rs11831920	0.83[EUR][1000 genomes]
rs11831929	0.83[EUR][1000 genomes]
rs11832316	0.83[EUR][1000 genomes]
rs11833393	0.88[EUR][1000 genomes]
rs11834607	0.88[EUR][1000 genomes]
rs11835517	0.83[EUR][1000 genomes]
rs11835974	0.83[EUR][1000 genomes]
rs11836940	0.83[EUR][1000 genomes]
rs11837104	0.83[EUR][1000 genomes]
rs12300125	0.88[EUR][1000 genomes]
rs12310635	0.85[EUR][1000 genomes]
rs12578813	0.90[EUR][1000 genomes]
rs12579089	0.90[EUR][1000 genomes]
rs12579348	0.83[EUR][1000 genomes]
rs12579976	0.83[EUR][1000 genomes]
rs12580092	0.90[EUR][1000 genomes]
rs12580356	0.90[EUR][1000 genomes]
rs12580488	0.93[EUR][1000 genomes]
rs12581205	0.88[EUR][1000 genomes]
rs12581311	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12581366	0.90[EUR][1000 genomes]
rs12582013	0.93[EUR][1000 genomes]
rs12582056	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12582476	0.90[EUR][1000 genomes]
rs17096991	0.88[EUR][1000 genomes]
rs17096995	0.83[EUR][1000 genomes]
rs17097009	0.83[EUR][1000 genomes]
rs17097022	0.83[EUR][1000 genomes]
rs17121410	0.88[EUR][1000 genomes]
rs17121412	0.83[EUR][1000 genomes]
rs17594275	0.93[EUR][1000 genomes]
rs17611638	0.90[EUR][1000 genomes]
rs1946175	0.88[EUR][1000 genomes]
rs2042058	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2193663	0.83[EUR][1000 genomes]
rs2216439	0.80[EUR][1000 genomes]
rs235600	0.89[AMR][1000 genomes]
rs235601	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs235602	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs235607	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs235610	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs235616	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs235617	0.88[AMR][1000 genomes]
rs235621	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs235622	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs235625	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs235626	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs235627	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2408576	0.83[EUR][1000 genomes]
rs2408577	0.88[EUR][1000 genomes]
rs2430937	0.88[EUR][1000 genomes]
rs2430939	0.88[EUR][1000 genomes]
rs2430940	0.88[EUR][1000 genomes]
rs2430941	0.88[EUR][1000 genomes]
rs2430942	0.88[EUR][1000 genomes]
rs2430943	0.88[EUR][1000 genomes]
rs2430946	0.83[EUR][1000 genomes]
rs2471588	0.88[EUR][1000 genomes]
rs2471594	0.88[EUR][1000 genomes]
rs2471601	0.88[EUR][1000 genomes]
rs2471602	0.88[EUR][1000 genomes]
rs2471605	0.88[EUR][1000 genomes]
rs2471608	0.88[EUR][1000 genomes]
rs2471617	0.88[EUR][1000 genomes]
rs2471618	0.88[EUR][1000 genomes]
rs28768973	0.88[EUR][1000 genomes]
rs2909411	0.88[EUR][1000 genomes]
rs2960450	0.88[EUR][1000 genomes]
rs34008890	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35096979	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4604970	0.83[EUR][1000 genomes]
rs4768125	0.81[EUR][1000 genomes]
rs4768741	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4768742	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768744	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56111534	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56152575	0.83[EUR][1000 genomes]
rs56181923	0.83[EUR][1000 genomes]
rs56271434	0.83[EUR][1000 genomes]
rs57370043	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57658610	0.88[EUR][1000 genomes]
rs58449317	0.83[EUR][1000 genomes]
rs58503088	0.83[EUR][1000 genomes]
rs58561072	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58813899	0.83[EUR][1000 genomes]
rs59903937	0.83[EUR][1000 genomes]
rs60191997	0.88[EUR][1000 genomes]
rs60669661	0.83[EUR][1000 genomes]
rs60681792	0.83[EUR][1000 genomes]
rs61072098	0.85[EUR][1000 genomes]
rs61355826	0.88[EUR][1000 genomes]
rs61641663	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7138914	0.83[EUR][1000 genomes]
rs7308386	0.83[EUR][1000 genomes]
rs7310326	0.88[EUR][1000 genomes]
rs73282109	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73290402	0.83[EUR][1000 genomes]
rs73291964	0.83[EUR][1000 genomes]
rs73291976	0.83[EUR][1000 genomes]
rs73291980	0.83[EUR][1000 genomes]
rs73292000	0.83[EUR][1000 genomes]
rs73292001	0.88[EUR][1000 genomes]
rs73293911	0.83[EUR][1000 genomes]
rs73293919	0.83[EUR][1000 genomes]
rs7484802	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7488464	0.88[EUR][1000 genomes]
rs765707	0.83[EUR][1000 genomes]
rs766794	0.90[EUR][1000 genomes]
rs7976710	0.83[EUR][1000 genomes]
rs9669050	0.88[EUR][1000 genomes]
rs977069	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049525	chr12:46721742-47264172	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv541486	chr12:46721742-47264172	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
3	esv3416674	chr12:46988689-47178369	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv558783	chr12:46996632-47144856	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv1845143	chr12:47051076-47431496	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	esv3434230	chr12:47077314-47077615	Weak transcription ZNF genes & repeats Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:47070000-47077400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr12:47071000-47080600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr12:47071800-47077400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr12:47074600-47083800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr12:47074800-47091200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr12:47075600-47078200	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr12:47076000-47077800	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
8	chr12:47076600-47077800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
9	chr12:47076800-47077400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr12:47076800-47077600	Strong transcription	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links