Variant report

Variant	rs4487844
Chromosome Location	chr9:72450107-72450108
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10868078	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11140320	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11140367	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11140440	0.84[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140465	0.84[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13291820	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34323568	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34607127	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35531946	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4439190	1.00[ASW][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.87[LWK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs4498618	1.00[CHB][hapmap];0.96[GIH][hapmap];0.89[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62569924	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62569926	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv1050920	chr9:72345297-72579301	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv831611	chr9:72361905-72512134	Weak transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv893438	chr9:72363992-72720438	Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4487844	KLF9	cis	parietal	SCAN
rs4487844	PTAR1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72440000-72451400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr9:72440600-72457600	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr9:72441600-72467200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr9:72442800-72457600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr9:72442800-72480200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr9:72445400-72450200	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr9:72445600-72450400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr9:72445800-72450600	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr9:72448600-72451000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr9:72448600-72451200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr9:72449000-72467200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr9:72449200-72450200	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr9:72449200-72451000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
14	chr9:72449400-72450600	Weak transcription	Fetal Thymus	thymus
15	chr9:72449400-72451200	Flanking Active TSS	Primary T cells from cord blood	blood

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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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