Variant report

Variant	rs1971518
Chromosome Location	chr1:47208081-47208082
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CYP4B1-1	chr1:47208001-47208805	NONHSAT003036

Extended variants
information (count: 76 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10158678	0.84[CEU][hapmap]
rs1025806	0.89[CEU][hapmap];0.85[GIH][hapmap]
rs1048380	0.89[CEU][hapmap];0.85[GIH][hapmap]
rs1075982	0.88[CEU][hapmap]
rs10789492	0.94[EUR][1000 genomes]
rs10789493	0.94[EUR][1000 genomes]
rs10890411	0.84[CEU][hapmap]
rs10890415	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10890416	0.94[EUR][1000 genomes]
rs11211344	0.82[CEU][hapmap]
rs11211349	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11211354	0.96[EUR][1000 genomes]
rs1150064	0.84[CEU][hapmap]
rs1150068	0.84[CEU][hapmap]
rs12094663	0.84[CEU][hapmap]
rs1258052	0.82[CEU][hapmap]
rs1258053	0.84[CEU][hapmap]
rs1258056	0.84[CEU][hapmap]
rs13417	0.83[CEU][hapmap]
rs1440485	0.84[CEU][hapmap]
rs1440486	0.89[CEU][hapmap]
rs1440490	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1440491	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17102355	0.89[CEU][hapmap]
rs17102428	0.88[CEU][hapmap]
rs1745377	0.84[CEU][hapmap]
rs1971519	0.94[CEU][hapmap];0.96[EUR][1000 genomes]
rs2083486	0.84[CEU][hapmap]
rs2119301	0.89[CEU][hapmap];0.88[GIH][hapmap]
rs2218189	0.84[CEU][hapmap]
rs2241862	0.84[CEU][hapmap]
rs2289447	0.89[CEU][hapmap]
rs2304745	0.89[CEU][hapmap];0.88[GIH][hapmap]
rs2405026	0.89[CEU][hapmap];0.88[GIH][hapmap]
rs2405030	0.84[CEU][hapmap]
rs3737731	0.89[CEU][hapmap];0.85[GIH][hapmap]
rs3766211	0.84[CEU][hapmap]
rs3766212	0.83[CEU][hapmap]
rs3766214	0.83[CEU][hapmap]
rs3766215	0.89[CEU][hapmap];0.85[GIH][hapmap]
rs3766217	0.89[CEU][hapmap];0.85[GIH][hapmap]
rs3766219	0.84[CEU][hapmap]
rs3766224	0.84[CEU][hapmap]
rs4272563	0.84[CEU][hapmap]
rs4274009	0.83[CEU][hapmap]
rs4412540	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs585257	0.84[CEU][hapmap]
rs611468	0.84[CEU][hapmap]
rs614486	0.84[CEU][hapmap]
rs61782590	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs618554	0.82[CEU][hapmap]
rs620431	0.89[CEU][hapmap]
rs625590	0.84[CEU][hapmap]
rs637760	0.82[CEU][hapmap]
rs6429607	0.84[CEU][hapmap]
rs6429608	0.83[EUR][1000 genomes]
rs6429609	0.86[EUR][1000 genomes]
rs6429610	0.95[EUR][1000 genomes]
rs647999	0.84[CEU][hapmap]
rs6667885	0.84[CEU][hapmap]
rs6670495	0.94[CEU][hapmap];0.94[EUR][1000 genomes]
rs6671124	0.84[CEU][hapmap]
rs6690193	0.93[EUR][1000 genomes]
rs723334	0.84[CEU][hapmap]
rs723690	0.94[CEU][hapmap];0.91[TSI][hapmap];0.96[EUR][1000 genomes]
rs7354865	0.89[CEU][hapmap]
rs7354894	0.94[CEU][hapmap];0.94[EUR][1000 genomes]
rs7412469	0.89[CEU][hapmap];0.88[GIH][hapmap]
rs744096	0.89[CEU][hapmap]
rs7519866	0.83[EUR][1000 genomes]
rs7534179	0.96[EUR][1000 genomes]
rs7553243	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001455	chr1:46828004-47326539	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv534950	chr1:46828004-47326539	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1013048	chr1:47132831-47377364	Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv534955	chr1:47132831-47377364	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1971518	LEPRE1	cis	parietal	SCAN
rs1971518	FAAH	cis	cerebellum	SCAN
rs1971518	TCTEX1D4	cis	parietal	SCAN
rs1971518	MKNK1	cis	cerebellum	SCAN
rs1971518	NSUN4	cis	cerebellum	SCAN
rs1971518	SLC6A9	cis	parietal	SCAN

Chromatin state (count:0 , 50 per page) page:

No data

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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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