Variant report

Variant	rs10271456
Chromosome Location	chr7:25498909-25498910
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10227290	1.00[ASN][1000 genomes]
rs10266599	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10266720	1.00[ASN][1000 genomes]
rs10270802	1.00[ASN][1000 genomes]
rs17151656	0.86[ASN][1000 genomes]
rs2079495	1.00[ASN][1000 genomes]
rs2391133	0.86[ASN][1000 genomes]
rs3857726	1.00[ASN][1000 genomes]
rs4722468	0.86[ASN][1000 genomes]
rs62452226	1.00[ASN][1000 genomes]
rs62452227	1.00[ASN][1000 genomes]
rs62452229	1.00[ASN][1000 genomes]
rs6958937	0.86[ASN][1000 genomes]
rs7794566	1.00[EUR][1000 genomes]
rs7795036	1.00[EUR][1000 genomes]
rs9969299	1.00[ASN][1000 genomes]
rs9969303	1.00[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	nsv606426	chr7:25254125-25621579	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1016813	chr7:25405859-26150509	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	108 gene(s)	inside rSNPs	diseases
3	nsv538803	chr7:25405859-26150509	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	108 gene(s)	inside rSNPs	diseases
4	nsv1033664	chr7:25471881-25503391	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv1033757	chr7:25472222-25504421	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10271456	SCGN	trans	brain	seeQTL
rs10271456	FLT3	trans	brain	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:25496800-25499200	Weak transcription	Psoas Muscle	Psoas
2	chr7:25496800-25500000	Weak transcription	Right Atrium	heart
3	chr7:25497000-25500000	Weak transcription	Liver	Liver
4	chr7:25497200-25500000	Weak transcription	Ovary	ovary
5	chr7:25498400-25499000	Enhancers	Gastric	stomach
6	chr7:25498600-25499000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr7:25498600-25499600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr7:25498800-25499000	Enhancers	Sigmoid Colon	Sigmoid Colon

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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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