Variant report

Variant	rs684476
Chromosome Location	chr9:92794619-92794620
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs4743823	0.81[YRI][hapmap]
rs4744020	0.80[MKK][hapmap]
rs496129	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs497510	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs552128	0.81[YRI][hapmap]
rs586750	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs652454	0.81[ASW][hapmap];0.89[CEU][hapmap];0.92[GIH][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];0.81[YRI][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs657899	0.94[ASW][hapmap];0.89[CEU][hapmap];0.92[GIH][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs661741	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7021437	0.89[AFR][1000 genomes]
rs7027342	0.88[AFR][1000 genomes]
rs7030563	0.81[YRI][hapmap]
rs7866392	0.80[GIH][hapmap]

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	nsv893561	chr9:92732368-92802101	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
2	nsv482303	chr9:92752928-92890226	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
3	nsv614852	chr9:92786722-93100550	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs684476	SYK	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:92788400-92794800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr9:92789600-92806400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr9:92789800-92796200	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr9:92789800-92796400	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr9:92789800-92799600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr9:92790000-92796400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr9:92792600-92795600	Enhancers	Brain Germinal Matrix	brain
8	chr9:92793000-92796400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr9:92793200-92795600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr9:92793200-92796400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr9:92793200-92796400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr9:92793200-92796600	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr9:92793600-92796600	Enhancers	Liver	Liver
14	chr9:92793800-92796800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr9:92794600-92795000	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr9:92794600-92795200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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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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