Variant report

Variant	rs2408616
Chromosome Location	chr12:47041915-47041916
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11183519	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11183551	0.86[AMR][1000 genomes]
rs12301825	0.81[AMR][1000 genomes]
rs12311952	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12318944	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12579010	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12579419	0.96[AMR][1000 genomes]
rs12579984	1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12580176	0.94[AMR][1000 genomes]
rs12581743	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1266371	0.84[AMR][1000 genomes]
rs17097079	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17097091	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs17097141	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1946174	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1986154	0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2160892	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2287470	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2897979	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4351902	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4768124	0.82[AMR][1000 genomes]
rs4768126	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4768738	0.96[ASN][1000 genomes]
rs4768740	1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4768747	0.87[ASN][1000 genomes]
rs4768749	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs57616927	0.96[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs58806862	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs59408501	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7132144	0.80[AMR][1000 genomes]
rs7133051	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7310614	0.98[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7311414	0.98[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7315740	0.98[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs73282105	0.98[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs73282110	0.98[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7487359	0.82[AMR][1000 genomes]
rs7959179	0.93[ASN][1000 genomes]
rs7971812	0.82[ASN][1000 genomes]
rs7976531	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7976785	0.80[AMR][1000 genomes]
rs7979449	0.82[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	nsv692	chr12:47018472-47049495	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	esv1844378	chr12:47028797-47072016	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:47032800-47042000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr12:47036800-47051400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr12:47041000-47044200	Weak transcription	HUVEC	blood vessel
4	chr12:47041000-47054200	Weak transcription	Fetal Kidney	kidney
5	chr12:47041600-47042200	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr12:47041600-47042200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
7	chr12:47041600-47042200	ZNF genes & repeats	Fetal Intestine Small	intestine

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