Variant report

Variant	rs11238240
Chromosome Location	chr7:53029072-53029073
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10268005	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11238241	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11761792	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11761819	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11763890	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12535959	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1813254	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56289347	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62446420	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6968538	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv888027	chr7:52588348-53190508	Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1017676	chr7:52932139-53350524	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv831001	chr7:53003534-53152783	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv607008	chr7:53009355-53068819	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region	1 gene(s)	inside rSNPs	diseases
5	nsv888034	chr7:53026365-53611898	Flanking Bivalent TSS/Enh Enhancers Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11238240	CCT6A	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:53023000-53031000	Enhancers	Placenta	Placenta
2	chr7:53023600-53040000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr7:53025600-53030000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr7:53026600-53030400	Enhancers	Placenta Amnion	Placenta Amnion
5	chr7:53027800-53029200	Weak transcription	HUVEC	blood vessel
6	chr7:53028200-53029600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr7:53028200-53029600	Weak transcription	Fetal Muscle Leg	muscle
8	chr7:53028200-53029600	Weak transcription	Ovary	ovary
9	chr7:53028800-53030800	Enhancers	Aorta	Aorta
10	chr7:53029000-53029200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr7:53029000-53029200	Flanking Active TSS	Fetal Heart	heart
12	chr7:53029000-53029200	Enhancers	Right Atrium	heart
13	chr7:53029000-53029600	Enhancers	Colon Smooth Muscle	Colon
14	chr7:53029000-53030800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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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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