Variant report

Variant	rs4916418
Chromosome Location	chr1:172034439-172034440
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10218579	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10752861	0.90[CHB][hapmap];0.82[ASN][1000 genomes]
rs12061795	0.86[EUR][1000 genomes]
rs12090953	0.90[CHB][hapmap];0.81[ASN][1000 genomes]
rs17346438	0.86[MEX][hapmap]
rs2761184	0.90[CHB][hapmap];0.83[CHD][hapmap]
rs2761186	0.90[CHB][hapmap]
rs2819531	0.90[CHB][hapmap]
rs4244191	0.90[CHB][hapmap];0.83[CHD][hapmap];0.82[ASN][1000 genomes]
rs4641331	0.90[CHB][hapmap];0.88[CHD][hapmap];0.82[ASN][1000 genomes]
rs4916242	0.90[CHB][hapmap]
rs4916416	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58503720	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6425637	0.90[CHB][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532342	chr1:171922237-172133785	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases
2	nsv3532	chr1:171997451-172042351	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4916418	XCL2	cis	parietal	SCAN
rs4916418	DCAF6	cis	cerebellum	SCAN
rs4916418	MPZL1	cis	parietal	SCAN
rs4916418	C1orf112	cis	cerebellum	SCAN
rs4916418	GORAB	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172010600-172051400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:172010800-172037600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr1:172011400-172037800	Weak transcription	Ovary	ovary
4	chr1:172015000-172042600	Weak transcription	Fetal Brain Female	brain
5	chr1:172016600-172037800	Weak transcription	Brain Substantia Nigra	brain
6	chr1:172020200-172038800	Weak transcription	Brain Angular Gyrus	brain
7	chr1:172020200-172040600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:172024600-172040400	Weak transcription	Brain Anterior Caudate	brain
9	chr1:172024800-172040600	Weak transcription	Brain Germinal Matrix	brain
10	chr1:172025200-172037600	Weak transcription	Brain Cingulate Gyrus	brain
11	chr1:172025200-172037800	Weak transcription	Brain Hippocampus Middle	brain
12	chr1:172025200-172040600	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr1:172025400-172037800	Weak transcription	Brain Inferior Temporal Lobe	brain

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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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