Variant report

Variant	rs2396135
Chromosome Location	chr7:109230184-109230185
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10246352	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1721434	0.85[ASN][1000 genomes]
rs1721435	0.80[ASN][1000 genomes]
rs1721438	0.89[ASN][1000 genomes]
rs1851827	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2091133	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2689963	0.87[ASN][1000 genomes]
rs2689964	0.87[ASN][1000 genomes]
rs35884256	0.80[ASN][1000 genomes]
rs62473271	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62473273	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62473274	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62473275	0.84[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	nsv1023379	chr7:109003574-109355234	Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv608079	chr7:109098364-109862289	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1020761	chr7:109208187-109275700	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3'	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
rs2396135	TMEM168	cis	cerebellum	SCAN
rs2396135	NRCAM	cis	parietal	SCAN
rs2396135	GPR22	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:109211800-109234000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr7:109221200-109234400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr7:109228400-109237800	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr7:109228800-109230200	Strong transcription	HUES6 Cell Line	embryonic stem cell
5	chr7:109228800-109231000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr7:109229400-109230200	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
7	chr7:109229600-109230800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr7:109229600-109231400	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr7:109229600-109234400	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr7:109230000-109230200	Enhancers	H1 Cell Line	embryonic stem cell
11	chr7:109230000-109231400	Active TSS	iPS-20b 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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