Variant report

Variant	rs2950916
Chromosome Location	chr8:35137310-35137311
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs13282296	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1534587	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2950892	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2950893	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2950895	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2950897	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2950898	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2950901	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2950909	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2950924	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2980378	0.88[EUR][1000 genomes]
rs2980391	0.82[EUR][1000 genomes]
rs2980403	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2980406	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2980408	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3108619	0.89[EUR][1000 genomes]
rs5000056	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017085	chr8:34742896-35594241	Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv539546	chr8:34742896-35594241	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv831284	chr8:35018419-35193084	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv429910	chr8:35021411-35257445	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2950916	UNC5D	cis	parietal	SCAN
rs2950916	LETM2	cis	cerebellum	SCAN
rs2950916	ASH2L	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:35116200-35139200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr8:35124400-35145200	Weak transcription	Fetal Brain Female	brain
3	chr8:35124600-35151200	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr8:35132400-35143800	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr8:35133800-35137400	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr8:35134400-35144000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr8:35135800-35139200	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr8:35135800-35143800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr8:35135800-35143800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr8:35135800-35144000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr8:35135800-35148800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr8:35136000-35143800	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr8:35136000-35143800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr8:35136600-35144000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr8:35136800-35144000	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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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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