Variant report

Variant	rs7419959
Chromosome Location	chr2:12220923-12220924
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10183374	0.95[ASN][1000 genomes]
rs10190465	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10495590	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12474091	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12997170	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3845756	0.85[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs62113831	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003899	chr2:11789374-12248081	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
2	nsv999704	chr2:12153766-12243960	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1005069	chr2:12161023-12242734	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1000696	chr2:12162843-12241022	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv997538	chr2:12216408-12242734	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7419959	LPIN1	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:12215400-12224200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr2:12217400-12223200	Weak transcription	Fetal Lung	lung
3	chr2:12217400-12249800	Weak transcription	GM12878-XiMat	blood
4	chr2:12217800-12223000	Weak transcription	Primary B cells from peripheral blood	blood
5	chr2:12218400-12222000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr2:12218600-12221600	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr2:12219600-12223600	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr2:12219800-12222000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr2:12220000-12223200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr2:12220000-12223200	Weak transcription	K562	blood
11	chr2:12220600-12222400	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr2:12220600-12223600	Enhancers	Primary T cells from cord blood	blood
13	chr2:12220800-12221800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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