Variant report

Variant	rs4540261
Chromosome Location	chr6:39448389-39448390
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 82 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10947813	0.92[ASN][1000 genomes]
rs11961693	0.88[ASN][1000 genomes]
rs11962587	0.89[CHB][hapmap];0.93[JPT][hapmap];0.99[ASN][1000 genomes]
rs11964924	0.89[CHB][hapmap];0.93[JPT][hapmap];0.96[ASN][1000 genomes]
rs11968279	0.81[ASN][1000 genomes]
rs11968704	0.89[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs11969059	0.94[CHB][hapmap];0.93[JPT][hapmap];0.96[ASN][1000 genomes]
rs11969395	0.98[ASN][1000 genomes]
rs1410488	0.83[ASN][1000 genomes]
rs1546910	0.90[CHB][hapmap]
rs16892158	0.89[CHB][hapmap];0.93[JPT][hapmap]
rs1927774	0.88[CHD][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs1927775	0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs1952362	0.88[CHD][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs2026670	0.83[CHB][hapmap];0.89[CHD][hapmap]
rs2073134	0.90[CHB][hapmap];0.81[CHD][hapmap]
rs2235817	0.89[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs2273063	0.89[CHB][hapmap];0.91[CHD][hapmap];0.83[ASN][1000 genomes]
rs2395727	0.83[ASN][1000 genomes]
rs28533484	0.96[ASN][1000 genomes]
rs35553201	0.85[ASN][1000 genomes]
rs4236064	0.89[CHB][hapmap];0.97[CHD][hapmap]
rs4464790	0.85[ASN][1000 genomes]
rs4482968	0.89[CHB][hapmap];0.88[ASN][1000 genomes]
rs4482969	0.88[ASN][1000 genomes]
rs4711598	0.84[CHB][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs4714253	0.84[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs4714254	0.83[ASN][1000 genomes]
rs4714255	0.89[CHB][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs4714256	0.94[CHB][hapmap];0.97[CHD][hapmap];0.80[MEX][hapmap];0.85[ASN][1000 genomes]
rs55860200	0.82[ASN][1000 genomes]
rs57703896	0.83[ASN][1000 genomes]
rs59724542	0.92[ASN][1000 genomes]
rs6901155	0.84[CHB][hapmap];0.81[CHD][hapmap]
rs6919556	0.81[CHB][hapmap]
rs9296298	0.89[CHD][hapmap]
rs9296299	0.89[CHB][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap];0.99[ASN][1000 genomes]
rs9296300	1.00[CHB][hapmap];0.94[CHD][hapmap];0.80[MEX][hapmap]
rs9349120	0.84[CHB][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs9357305	0.84[ASN][1000 genomes]
rs9357307	0.94[CHB][hapmap]
rs9357308	0.89[CHB][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs9357309	0.89[CHB][hapmap];0.87[ASN][1000 genomes]
rs9367008	0.94[CHB][hapmap];0.93[JPT][hapmap]
rs9367009	0.94[CHB][hapmap];0.93[JPT][hapmap];0.98[ASN][1000 genomes]
rs9367012	0.89[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs9367016	0.88[ASN][1000 genomes]
rs9369117	0.84[ASN][1000 genomes]
rs9369119	1.00[CHB][hapmap];0.94[CHD][hapmap];0.80[MEX][hapmap]
rs9369122	0.81[CHB][hapmap]
rs9369123	0.83[ASN][1000 genomes]
rs9369124	0.82[ASN][1000 genomes]
rs9380861	0.91[ASN][1000 genomes]
rs9380862	0.83[ASN][1000 genomes]
rs9380863	0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs9380864	0.84[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs9380865	0.84[CHB][hapmap];0.93[JPT][hapmap];0.94[ASN][1000 genomes]
rs9380867	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs9380868	0.94[CHB][hapmap];0.91[JPT][hapmap]
rs9380871	0.88[ASN][1000 genomes]
rs9380872	0.88[ASN][1000 genomes]
rs9380873	0.89[CHB][hapmap];0.88[ASN][1000 genomes]
rs9380874	0.89[CHB][hapmap]
rs9380880	0.85[CHD][hapmap]
rs9394592	0.84[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.85[TSI][hapmap];0.91[ASN][1000 genomes]
rs9394594	0.84[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap]
rs9394595	0.84[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.94[ASN][1000 genomes]
rs9394598	0.89[CHB][hapmap];0.93[JPT][hapmap]
rs9394599	0.94[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap]
rs9394600	0.89[CHB][hapmap];0.93[JPT][hapmap];0.98[ASN][1000 genomes]
rs9394601	0.85[ASN][1000 genomes]
rs9394602	0.89[CHB][hapmap];0.87[ASN][1000 genomes]
rs9394603	0.87[ASN][1000 genomes]
rs9394606	0.89[CHB][hapmap];0.83[ASN][1000 genomes]
rs9394609	0.82[CHD][hapmap]
rs9394616	0.82[JPT][hapmap]
rs9462553	0.94[CHB][hapmap]
rs9471103	0.83[ASN][1000 genomes]
rs9471113	0.94[CHB][hapmap]

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	nsv885822	chr6:39327708-39721216	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv428145	chr6:39404129-39460795	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv885823	chr6:39421715-39526867	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4540261	SRPK1	cis	cerebellum	SCAN
rs4540261	ETV7	cis	parietal	SCAN
rs4540261	LOC221442	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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