Variant report

Variant	rs12469378
Chromosome Location	chr2:173568165-173568166
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1010752	0.82[ASN][1000 genomes]
rs10930561	0.80[CHB][hapmap]
rs10930566	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10930567	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10930568	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10930569	0.81[ASN][1000 genomes]
rs12052531	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12464110	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12465512	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12465795	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12617037	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12617921	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12618078	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12618132	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12620518	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12621044	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13423020	0.82[ASN][1000 genomes]
rs1530864	0.80[CHB][hapmap]
rs1530865	0.80[CHB][hapmap]
rs1531148	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1531149	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16860693	0.80[CHB][hapmap]
rs16860781	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16860789	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16860834	1.00[AFR][1000 genomes]
rs2122833	0.95[EUR][1000 genomes]
rs28761282	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4395226	0.82[ASN][1000 genomes]
rs59578456	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59606385	1.00[AFR][1000 genomes]
rs60127617	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61121406	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6433376	0.81[ASN][1000 genomes]
rs6709144	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6718681	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6719140	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6733671	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs836628	0.84[ASN][1000 genomes]
rs836643	0.95[EUR][1000 genomes];0.90[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	nsv533927	chr2:173161637-173796894	Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	esv2760591	chr2:173396905-173719520	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv583665	chr2:173460640-173643087	Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 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	chr2:173564000-173571600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr2:173564200-173575600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:173565800-173577200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:173566000-173569000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr2:173566000-173575400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr2:173566800-173568200	Enhancers	Fetal Brain Male	brain
7	chr2:173566800-173568800	Weak transcription	Osteobl	bone
8	chr2:173567000-173568800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr2:173567000-173568800	Weak transcription	NHEK	skin
10	chr2:173568000-173568800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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