Variant report

Variant	rs56088348
Chromosome Location	chr12:2145788-2145789
allele	A/C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:2145401..2146012-chr12:2691847..2692721,2	MCF-7	breast:
2	chr12:2144090..2145938-chr12:2158684..2161227,2	MCF-7	breast:
3	chr12:2144515..2146674-chr12:2148962..2151800,2	K562	blood:
4	chr12:2145583..2146140-chr12:2391449..2392036,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151067	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs2429149	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55683572	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55745807	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55751814	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55762621	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55895736	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55964304	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56101318	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56305330	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73044413	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73044427	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73044433	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73044434	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73044436	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73044444	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73044446	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73044447	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73044457	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73044476	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73044478	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73044480	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73046444	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73046451	0.86[AMR][1000 genomes]
rs73048359	1.00[AFR][1000 genomes]
rs7956039	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7958309	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7958898	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7970196	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7971903	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7976547	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948480	chr12:1776217-2284333	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv898598	chr12:1939252-2215448	Strong transcription Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv1040370	chr12:2021395-2671017	Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv948400	chr12:2022411-2601363	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv521838	chr12:2060580-2299680	Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1035885	chr12:2077660-2310157	Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv541350	chr12:2077660-2310157	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv1038722	chr12:2085035-2308205	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv541351	chr12:2085035-2308205	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv898601	chr12:2124955-2215448	Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv826182	chr12:2136395-2208074	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:2143200-2149000	Enhancers	Fetal Heart	heart
2	chr12:2143800-2146800	Enhancers	Left Ventricle	heart
3	chr12:2144800-2151000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr12:2144800-2157600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr12:2145000-2148800	Weak transcription	Right Atrium	heart
6	chr12:2145200-2147800	Weak transcription	Rectal Smooth Muscle	rectum
7	chr12:2145400-2146200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
8	chr12:2145600-2146200	Weak transcription	Right Ventricle	heart
9	chr12:2145600-2147800	Weak transcription	Colon Smooth Muscle	Colon

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