Variant report

Variant	rs3980072
Chromosome Location	chr2:113371883-113371884
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CHCHD5-2	chr2:113371790-113372008	ENSG00000243389.1

Extended variants
information (count: 21 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12987250	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13025131	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17586834	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17587043	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17647292	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28819453	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34015418	0.90[EUR][1000 genomes]
rs35547295	0.82[AMR][1000 genomes]
rs35670704	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs36082214	0.91[EUR][1000 genomes]
rs3980073	0.86[EUR][1000 genomes]
rs3980074	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6737981	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6743603	0.86[EUR][1000 genomes]
rs71414685	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7566777	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7607685	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7607817	0.89[AMR][1000 genomes];0.93[EUR][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	nsv874877	chr2:113287964-113382054	Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
2	nsv458997	chr2:113313794-113431092	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv582708	chr2:113313794-113431092	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3980072	AC079922.3	cis	Muscle Skeletal	GTEx
rs3980072	AC079922.3	cis	lung	GTEx
rs3980072	AC079922.3	cis	Artery Aorta	GTEx
rs3980072	AC079922.3	cis	Heart Left Ventricle	GTEx
rs3980072	AC079922.3	cis	Artery Tibial	GTEx
rs3980072	AC079922.3	cis	Esophagus Mucosa	GTEx
rs3980072	AC079922.3	cis	Thyroid	GTEx

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113346800-113374600	Weak transcription	Ovary	ovary
2	chr2:113348600-113383600	Weak transcription	Brain Cingulate Gyrus	brain
3	chr2:113349000-113384000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr2:113357800-113375200	Weak transcription	Stomach Smooth Muscle	stomach
5	chr2:113357800-113384200	Weak transcription	Pancreas	Pancrea
6	chr2:113358000-113384000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr2:113359800-113372000	Weak transcription	Fetal Brain Female	brain
8	chr2:113364600-113372800	Weak transcription	Fetal Stomach	stomach
9	chr2:113365600-113372000	Weak transcription	Brain Anterior Caudate	brain
10	chr2:113370000-113372200	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr2:113370400-113383800	Weak transcription	Fetal Muscle Leg	muscle
12	chr2:113370600-113377800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr2:113371000-113372000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr2:113371400-113372000	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr2:113371600-113372000	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr2:113371600-113372200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr2:113371600-113372800	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr2:113371600-113372800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:113371600-113372800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr2:113371600-113374000	Enhancers	HepG2	liver
21	chr2:113371600-113382000	Weak transcription	Spleen	Spleen
22	chr2:113371800-113372000	Enhancers	H9 Cell Line	embryonic stem cell
23	chr2:113371800-113372000	Enhancers	HUES48 Cell Line	embryonic stem cell
24	chr2:113371800-113372000	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr2:113371800-113372000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr2:113371800-113372200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr2:113371800-113372200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
28	chr2:113371800-113372200	Enhancers	Fetal Intestine Small	intestine
29	chr2:113371800-113372200	ZNF genes & repeats	Fetal Muscle Trunk	muscle
30	chr2:113371800-113372400	Genic enhancers	Gastric	stomach
31	chr2:113371800-113372600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr2:113371800-113372600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr2:113371800-113373000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr2:113371800-113373200	Enhancers	H1 Cell Line	embryonic stem cell
35	chr2:113371800-113373200	Enhancers	iPS-20b Cell Line	embryonic stem cell
36	chr2:113371800-113373200	Strong transcription	Brain Germinal Matrix	brain

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