Variant report

Variant	rs73044480
Chromosome Location	chr12:2158469-2158470
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LRTM2-3	chr12:2158300-2158629	ENSG00000256257.1

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs2429149	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55683572	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55745807	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55751814	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55762621	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55895736	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55964304	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56018122	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs56088348	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56101318	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56305330	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73044413	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73044427	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73044433	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73044434	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73044436	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73044444	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73044446	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73044447	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73044457	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73044476	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73044478	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73046444	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73046451	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs73046455	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73046458	1.00[AFR][1000 genomes]
rs7956039	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7958309	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7958898	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7970196	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7971903	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7976547	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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
12	nsv826183	chr12:2147469-2257818	Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv898602	chr12:2149786-2223740	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:2155800-2160400	Weak transcription	Right Ventricle	heart
2	chr12:2157000-2158800	Weak transcription	Fetal Heart	heart
3	chr12:2157600-2159200	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr12:2157800-2158600	Enhancers	HepG2	liver
5	chr12:2157800-2159000	Enhancers	Fetal Intestine Small	intestine
6	chr12:2157800-2159400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
7	chr12:2157800-2159800	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr12:2158000-2158800	Enhancers	Fetal Intestine Large	intestine
9	chr12:2158000-2160600	Weak transcription	Left Ventricle	heart
10	chr12:2158000-2160800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr12:2158200-2159200	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr12:2158200-2159200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr12:2158200-2159800	Enhancers	Osteobl	bone
14	chr12:2158400-2159000	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr12:2158400-2159600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
16	chr12:2158400-2159600	Enhancers	NHDF-Ad	bronchial

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