Variant report

Variant	rs1019748
Chromosome Location	chr5:5214077-5214078
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1428023	1.00[CHB][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1467954	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2913615	1.00[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2964443	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4702247	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6555337	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.82[TSI][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6895855	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6898726	0.89[EUR][1000 genomes];0.94[ASN][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	nsv1024784	chr5:4980979-5391231	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv1032719	chr5:5102763-5387406	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv537621	chr5:5102763-5387406	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1019748	LPCAT1	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:5185200-5262800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr5:5193800-5219000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr5:5199000-5240000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr5:5199800-5228200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr5:5200200-5252800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr5:5201400-5223000	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr5:5201400-5226000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr5:5202600-5240200	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr5:5205400-5222400	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr5:5209600-5221000	Weak transcription	Ovary	ovary
11	chr5:5209600-5222000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr5:5210000-5220800	Weak transcription	NH-A	brain
13	chr5:5210200-5217800	Weak transcription	Fetal Kidney	kidney
14	chr5:5210200-5218400	Weak transcription	Psoas Muscle	Psoas
15	chr5:5214000-5214200	Enhancers	Pancreas	Pancrea

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Input of quick search could be:

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

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