Variant report

Variant	rs1421214
Chromosome Location	chr8:39843720-39843721
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10104711	0.87[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.84[ASN][1000 genomes]
rs1362849	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2015592	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs2543072	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2729472	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2729478	0.94[ASN][1000 genomes]
rs2729482	0.87[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.84[ASN][1000 genomes]
rs888444	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv539555	chr8:39683857-40673606	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1033371	chr8:39749437-39899540	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1421214	LSM1	cis	parietal	SCAN
rs1421214	DDHD2	cis	cerebellum	SCAN
rs1421214	HGSNAT	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:39835200-39853600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr8:39836200-39847400	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr8:39837000-39847200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr8:39837600-39847600	Weak transcription	Right Atrium	heart
5	chr8:39839200-39845200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr8:39840400-39847800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr8:39842400-39847800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr8:39842800-39844600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr8:39843000-39847600	Weak transcription	Liver	Liver
10	chr8:39843000-39847600	Weak transcription	Hela-S3	cervix
11	chr8:39843000-39853000	Weak transcription	Lung	lung
12	chr8:39843400-39847600	Weak transcription	Fetal Heart	heart

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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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