Variant report

Variant	rs73412484
Chromosome Location	chr15:45752892-45752893
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:45751428..45753580-chr15:45925996..45928453,2	MCF-7	breast:
2	chr15:45750236..45753171-chr15:45878645..45880450,2	MCF-7	breast:
3	chr15:45751814..45754507-chr15:45754851..45757690,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C15orf48-1	chr15:45752644-45753154	ENSG00000259354.1

Variant related genes	Relation type
ENSG00000137767	Chromatin interaction
ENSG00000260170	Chromatin interaction
ENSG00000104164	Chromatin interaction

Extended variants
information (count: 151 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:142)

rs_ID	r²[population]
rs1005072	1.00[EUR][1000 genomes]
rs10152775	0.92[AMR][1000 genomes]
rs10152792	0.92[AMR][1000 genomes]
rs1153836	1.00[EUR][1000 genomes]
rs1153837	1.00[EUR][1000 genomes]
rs1153839	1.00[EUR][1000 genomes]
rs1153840	1.00[EUR][1000 genomes]
rs1153841	1.00[EUR][1000 genomes]
rs1153842	1.00[EUR][1000 genomes]
rs1153843	1.00[EUR][1000 genomes]
rs1153844	1.00[EUR][1000 genomes]
rs1288647	1.00[EUR][1000 genomes]
rs1288848	1.00[EUR][1000 genomes]
rs1288849	1.00[EUR][1000 genomes]
rs1288850	1.00[EUR][1000 genomes]
rs1288851	1.00[EUR][1000 genomes]
rs1288853	1.00[EUR][1000 genomes]
rs1288854	1.00[EUR][1000 genomes]
rs1288855	1.00[EUR][1000 genomes]
rs1288856	1.00[EUR][1000 genomes]
rs1288857	1.00[EUR][1000 genomes]
rs1288858	1.00[EUR][1000 genomes]
rs1288859	1.00[EUR][1000 genomes]
rs1288864	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1295500	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1295501	1.00[EUR][1000 genomes]
rs1426933	1.00[EUR][1000 genomes]
rs1426934	1.00[EUR][1000 genomes]
rs1529353	0.92[AMR][1000 genomes]
rs1529354	0.85[AMR][1000 genomes]
rs1547488	1.00[EUR][1000 genomes]
rs1547489	1.00[EUR][1000 genomes]
rs1547490	1.00[EUR][1000 genomes]
rs1559891	1.00[EUR][1000 genomes]
rs1559892	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1629849	1.00[EUR][1000 genomes]
rs1629871	1.00[EUR][1000 genomes]
rs1648875	1.00[EUR][1000 genomes]
rs16943587	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16943691	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16943731	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16944196	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16944305	0.85[AMR][1000 genomes]
rs16945588	0.85[AMR][1000 genomes]
rs16945605	0.85[AMR][1000 genomes]
rs1768457	1.00[EUR][1000 genomes]
rs1834689	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1834691	1.00[EUR][1000 genomes]
rs1970374	0.92[AMR][1000 genomes]
rs2059661	1.00[EUR][1000 genomes]
rs2059662	1.00[EUR][1000 genomes]
rs2412958	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2433613	1.00[EUR][1000 genomes]
rs2433614	1.00[EUR][1000 genomes]
rs2433615	1.00[EUR][1000 genomes]
rs2433622	1.00[EUR][1000 genomes]
rs2433623	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2433624	1.00[EUR][1000 genomes]
rs2433625	1.00[EUR][1000 genomes]
rs2433626	1.00[EUR][1000 genomes]
rs2433627	1.00[EUR][1000 genomes]
rs2433628	1.00[EUR][1000 genomes]
rs2453514	1.00[EUR][1000 genomes]
rs2453516	1.00[EUR][1000 genomes]
rs2453517	1.00[EUR][1000 genomes]
rs2453519	1.00[EUR][1000 genomes]
rs2453520	1.00[EUR][1000 genomes]
rs2453521	1.00[EUR][1000 genomes]
rs2453549	1.00[EUR][1000 genomes]
rs2467861	1.00[EUR][1000 genomes]
rs2467874	1.00[EUR][1000 genomes]
rs2467875	1.00[EUR][1000 genomes]
rs2467876	1.00[EUR][1000 genomes]
rs2467878	1.00[EUR][1000 genomes]
rs2467879	1.00[EUR][1000 genomes]
rs2467880	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2467882	1.00[EUR][1000 genomes]
rs2467883	1.00[EUR][1000 genomes]
rs2467884	1.00[EUR][1000 genomes]
rs2467885	1.00[EUR][1000 genomes]
rs2467886	1.00[EUR][1000 genomes]
rs2467887	1.00[EUR][1000 genomes]
rs2467889	1.00[EUR][1000 genomes]
rs2486279	1.00[EUR][1000 genomes]
rs2486283	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2486284	1.00[EUR][1000 genomes]
rs3858908	0.92[AMR][1000 genomes]
rs57255527	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57263027	0.85[AMR][1000 genomes]
rs57421622	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58694071	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61169737	0.92[AMR][1000 genomes]
rs61756712	0.92[AMR][1000 genomes]
rs6493153	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs679569	0.85[AMR][1000 genomes]
rs7163098	0.85[AMR][1000 genomes]
rs7165846	0.92[AMR][1000 genomes]
rs7166434	0.85[AMR][1000 genomes]
rs7168672	0.92[AMR][1000 genomes]
rs7170941	0.92[AMR][1000 genomes]
rs7173046	0.92[AMR][1000 genomes]
rs73410550	1.00[EUR][1000 genomes]
rs73410575	1.00[EUR][1000 genomes]
rs73410577	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73412436	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73412437	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73412438	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73412440	1.00[EUR][1000 genomes]
rs73412443	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73412445	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73412447	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73412449	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73412452	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73412453	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73412454	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73412456	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73412457	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73412459	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73412460	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73412462	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73412463	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73412466	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73412467	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73412470	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73412473	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73412479	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73412488	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73412490	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73414454	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73414486	0.92[AMR][1000 genomes]
rs73416403	0.92[AMR][1000 genomes]
rs73416407	0.92[AMR][1000 genomes]
rs73416479	0.92[AMR][1000 genomes]
rs73416487	0.92[AMR][1000 genomes]
rs7495403	0.92[AMR][1000 genomes]
rs8029983	0.92[AMR][1000 genomes]
rs8034420	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8042179	0.92[AMR][1000 genomes]
rs937323	1.00[EUR][1000 genomes]
rs937324	1.00[EUR][1000 genomes]
rs937325	1.00[EUR][1000 genomes]
rs9672808	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916374	chr15:45058112-45769052	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv932147	chr15:45319178-45872076	Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv569315	chr15:45446156-45772448	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
4	nsv469721	chr15:45608881-45788002	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
5	nsv482380	chr15:45608881-45788002	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
6	nsv1523	chr15:45749900-45783825	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	esv3438002	chr15:45751960-45758158	Weak transcription Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	esv3413319	chr15:45752360-45757258	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
9	esv3445023	chr15:45752360-45757258	Weak transcription Strong transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45749200-45753200	Weak transcription	Gastric	stomach
2	chr15:45749400-45753200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:45749400-45753200	Weak transcription	Esophagus	oesophagus
4	chr15:45749400-45753200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr15:45749800-45753800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr15:45750600-45753200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr15:45750600-45753600	Weak transcription	Pancreas	Pancrea
8	chr15:45750800-45781000	Weak transcription	Stomach Mucosa	stomach
9	chr15:45751200-45753200	Weak transcription	Colonic Mucosa	Colon
10	chr15:45751200-45753200	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr15:45751200-45760000	Weak transcription	Fetal Stomach	stomach
12	chr15:45751200-45761200	Weak transcription	Fetal Intestine Small	intestine
13	chr15:45751200-45801600	Weak transcription	Rectal Smooth Muscle	rectum
14	chr15:45751400-45753600	Weak transcription	Fetal Kidney	kidney
15	chr15:45751600-45753400	Weak transcription	Duodenum Mucosa	Duodenum
16	chr15:45751600-45753600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr15:45752800-45754200	Strong transcription	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links