Variant report

Variant	rs11140349
Chromosome Location	chr9:86675587-86675588
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11140308	1.00[GIH][hapmap]
rs11140310	1.00[GIH][hapmap]
rs11140316	1.00[GIH][hapmap]
rs11140343	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11140344	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11140347	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11140351	0.94[ASN][1000 genomes]
rs11140354	0.94[ASN][1000 genomes]
rs11140355	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs11140358	0.91[ASN][1000 genomes]
rs11140359	0.91[ASN][1000 genomes]
rs11533048	0.91[ASN][1000 genomes]
rs11559389	0.89[ASN][1000 genomes]
rs12236797	0.91[ASN][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	nsv831644	chr9:86534310-86704395	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv893514	chr9:86584160-86678917	Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv614762	chr9:86625243-86700593	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1045322	chr9:86666993-86701912	Weak transcription Enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11140349	HSPA6	trans	brain	seeQTL
rs11140349	RBPMS	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86672000-86676600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr9:86672800-86676400	Weak transcription	Psoas Muscle	Psoas
3	chr9:86673000-86676600	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr9:86673400-86676600	Weak transcription	Fetal Muscle Leg	muscle
5	chr9:86673400-86677000	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr9:86675200-86676400	Weak transcription	Rectal Mucosa Donor 31	rectum

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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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