Variant report

Variant	rs8140229
Chromosome Location	chr22:28586674-28586675
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1303845	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes]
rs134172	0.90[AFR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs134179	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs134180	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap];0.97[AFR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs134183	0.95[CEU][hapmap]
rs134188	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs134196	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs134489	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes]
rs134500	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.80[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs134507	1.00[CEU][hapmap];0.90[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap]
rs138683	0.85[YRI][hapmap]
rs2223370	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4822952	0.86[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4822954	0.83[EUR][1000 genomes]
rs715517	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7284814	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8138645	0.89[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	nsv1062877	chr22:28163507-28866350	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv459866	chr22:28540492-28753833	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv588879	chr22:28540492-28753833	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs8140229	SEC14L4	cis	parietal	SCAN
rs8140229	TTC28	cis	cerebellum	SCAN
rs8140229	TTC28	cis	lymphoblastoid	seeQTL

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28572200-28597800	Weak transcription	Dnd41	blood
2	chr22:28577000-28603600	Weak transcription	Aorta	Aorta
3	chr22:28577800-28600400	Weak transcription	Right Atrium	heart
4	chr22:28579600-28587400	Weak transcription	Lung	lung
5	chr22:28583800-28589000	Weak transcription	Fetal Lung	lung
6	chr22:28585000-28587000	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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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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