Variant report

Variant	rs6531915
Chromosome Location	chr4:87240020-87240021
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 89 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10010751	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs10010952	0.81[CHB][hapmap];0.81[ASN][1000 genomes]
rs10011429	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs10856859	0.81[ASN][1000 genomes]
rs11097104	0.82[CHB][hapmap];0.80[ASN][1000 genomes]
rs11097105	0.81[ASN][1000 genomes]
rs11097106	0.82[CHB][hapmap];0.97[CHD][hapmap];0.85[MKK][hapmap];0.81[ASN][1000 genomes]
rs11097107	0.80[ASN][1000 genomes]
rs11097108	0.80[ASN][1000 genomes]
rs11097109	0.82[CHB][hapmap];0.97[CHD][hapmap];0.84[MKK][hapmap];0.81[ASN][1000 genomes]
rs1115229	0.81[ASN][1000 genomes]
rs11736313	0.81[ASN][1000 genomes]
rs12513293	0.81[ASN][1000 genomes]
rs13110630	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs13111170	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs13115030	0.82[CHB][hapmap]
rs13115172	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs13115429	0.82[CHB][hapmap]
rs13138286	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs13146797	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs13146802	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs1318492	0.81[ASN][1000 genomes]
rs1460755	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs17011705	0.81[ASN][1000 genomes]
rs28661214	0.81[ASN][1000 genomes]
rs2869430	0.81[ASN][1000 genomes]
rs2869432	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs2869437	0.80[ASN][1000 genomes]
rs2869438	0.82[CHB][hapmap];0.97[CHD][hapmap];0.80[ASN][1000 genomes]
rs2869439	0.81[ASN][1000 genomes]
rs28695505	0.81[ASN][1000 genomes]
rs2904093	0.81[ASN][1000 genomes]
rs2904096	0.82[CHB][hapmap];0.97[CHD][hapmap];0.82[MKK][hapmap]
rs2904097	0.82[CHB][hapmap]
rs2904099	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs2904100	0.81[CHB][hapmap];0.81[ASN][1000 genomes]
rs2904101	0.80[ASN][1000 genomes]
rs34683010	0.81[ASN][1000 genomes]
rs35324025	0.81[ASN][1000 genomes]
rs35443953	0.81[ASN][1000 genomes]
rs4371581	0.81[ASN][1000 genomes]
rs4693142	0.82[CHB][hapmap];0.97[CHD][hapmap];0.81[ASN][1000 genomes]
rs4693143	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs4693144	0.82[CHB][hapmap]
rs4693764	0.81[ASN][1000 genomes]
rs4693765	0.82[CHB][hapmap];0.97[CHD][hapmap];0.81[ASN][1000 genomes]
rs4693766	0.82[CHB][hapmap];0.97[CHD][hapmap];0.81[ASN][1000 genomes]
rs6531918	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs6531921	0.81[ASN][1000 genomes]
rs6531922	0.81[ASN][1000 genomes]
rs6531923	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs6531924	0.81[ASN][1000 genomes]
rs6825707	0.82[CHD][hapmap];0.81[MKK][hapmap]
rs6829923	0.81[ASN][1000 genomes]
rs6839160	0.81[ASN][1000 genomes]
rs6851604	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs6852305	0.81[ASN][1000 genomes]
rs6858306	0.81[ASN][1000 genomes]
rs7666454	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs7667999	0.81[ASN][1000 genomes]
rs7674849	0.82[CHB][hapmap]
rs7682129	0.80[CHD][hapmap]
rs7684258	0.80[CHB][hapmap]
rs7687972	0.81[ASN][1000 genomes]
rs7689808	0.82[CHB][hapmap];0.97[CHD][hapmap];0.81[ASN][1000 genomes]
rs7690323	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs7690384	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs7691172	0.81[ASN][1000 genomes]
rs7691626	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs7694034	0.82[CHB][hapmap];0.97[CHD][hapmap];0.82[MKK][hapmap];0.80[ASN][1000 genomes]
rs7694920	0.86[CHB][hapmap]
rs7699065	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs7699105	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs7699555	0.81[ASN][1000 genomes]
rs9307017	0.80[ASN][1000 genomes]
rs9654156	0.81[ASN][1000 genomes]
rs9654157	0.81[ASN][1000 genomes]
rs9990599	0.81[ASN][1000 genomes]
rs9994931	0.82[CHB][hapmap];0.97[CHD][hapmap];0.83[MKK][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003585	chr4:86957967-87250436	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv594786	chr4:87076360-87609320	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
3	nsv999470	chr4:87165663-87514552	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
4	nsv537164	chr4:87165663-87514552	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
5	nsv934210	chr4:87197339-87325578	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1011494	chr4:87221480-87257453	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv594787	chr4:87221827-87888667	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
8	nsv1007891	chr4:87230601-87252524	Strong transcription Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv461574	chr4:87239764-87279096	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv594788	chr4:87239764-87279096	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6531915	HSD17B11	cis	cerebellum	SCAN
rs6531915	PKD2	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87224000-87242600	Weak transcription	Fetal Stomach	stomach
2	chr4:87232600-87247400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr4:87235200-87250200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr4:87235800-87242200	Weak transcription	Fetal Brain Male	brain
5	chr4:87239200-87240800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr4:87239400-87252400	Weak transcription	Brain Angular Gyrus	brain
7	chr4:87239400-87254400	Weak transcription	Brain Hippocampus Middle	brain
8	chr4:87239400-87258600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr4:87240000-87241800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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