Variant report

Variant	rs567645
Chromosome Location	chr10:89957995-89957996
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1147648	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1929318	0.91[ASN][1000 genomes]
rs1943987	0.81[EUR][1000 genomes]
rs473875	0.84[ASN][1000 genomes]
rs485396	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs508901	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs510559	0.97[ASN][1000 genomes]
rs533722	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs535541	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs537546	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs543338	0.88[ASW][hapmap];1.00[CEU][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.96[TSI][hapmap];0.93[EUR][1000 genomes]
rs545874	0.82[ASN][1000 genomes]
rs551265	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs629959	0.81[EUR][1000 genomes]
rs645516	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs647730	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs7898930	0.90[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831940	chr10:89811247-89989199	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs567645	SNCG	cis	parietal	SCAN
rs567645	ANKRD1	cis	cerebellum	SCAN
rs567645	LRIT2	cis	cerebellum	SCAN
rs567645	CD7	trans	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:89951000-89965600	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr10:89955200-89960000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr10:89955400-89959200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr10:89955400-89960400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr10:89955400-89962400	Weak transcription	Left Ventricle	heart
6	chr10:89955400-89963800	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr10:89955400-89965000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr10:89955400-89998000	Weak transcription	Aorta	Aorta
9	chr10:89956200-89959600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr10:89956400-89959200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr10:89956400-89960000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr10:89956600-89960400	Weak transcription	Fetal Muscle Leg	muscle
13	chr10:89957600-89958600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr10:89957600-89958600	Enhancers	HMEC	breast
15	chr10:89957800-89958600	Enhancers	NHEK	skin

Quick Search:

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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