Variant report

Variant	rs6942775
Chromosome Location	chr7:38590458-38590459
allele	C/T
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]
rs10499602	1.00[ASN][1000 genomes]
rs11763360	0.98[ASN][1000 genomes]
rs1561309	1.00[ASN][1000 genomes]
rs1982179	1.00[ASN][1000 genomes]
rs2118460	0.87[AFR][1000 genomes]
rs2118461	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2164837	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35099182	0.85[ASN][1000 genomes]
rs4720290	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62444214	1.00[ASN][1000 genomes]
rs62444215	1.00[ASN][1000 genomes]
rs62444216	0.98[ASN][1000 genomes]
rs62444217	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	nsv932229	chr7:38248340-38727527	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
2	nsv830966	chr7:38393663-38602553	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1018890	chr7:38557432-38600944	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6942775	LOC648852	N/A	lymphoblastoid	RTeQTL

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:38587400-38596000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr7:38587600-38598000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr7:38589000-38591000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr7:38590200-38592000	Enhancers	Brain Germinal Matrix	brain
5	chr7:38590400-38591000	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr7:38590400-38591000	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr7:38590400-38591400	Enhancers	H1 Cell Line	embryonic stem cell
8	chr7:38590400-38591600	Enhancers	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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