Variant report

Variant	rs184580
Chromosome Location	chr15:76327581-76327582
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs12910576	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12915012	0.82[AMR][1000 genomes]
rs1391894	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs1695378	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1699263	0.92[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs189197	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2255701	0.93[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2441929	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2455899	0.93[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap];0.96[YRI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2460798	0.93[ASW][hapmap];0.93[CEU][hapmap];0.92[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2460800	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2469039	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2593277	0.80[EUR][1000 genomes]
rs2593278	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2593280	1.00[ASW][hapmap];0.93[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28876229	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2955733	1.00[GIH][hapmap]
rs2959842	1.00[GIH][hapmap]
rs2959852	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs334930	1.00[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs334934	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs334936	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs335681	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs335697	0.93[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs335706	0.91[CEU][hapmap];0.92[JPT][hapmap];0.95[YRI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs335711	0.93[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4886747	0.81[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];0.92[GIH][hapmap];0.92[JPT][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap]
rs4886753	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4886754	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs71403522	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8024155	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs985849	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]

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	nsv531903	chr15:75889302-76342128	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv904398	chr15:76220285-76359055	Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv569998	chr15:76232605-76550938	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs184580	LRRC49	cis	cerebellum	SCAN
rs184580	NRG4	cis	cerebellum	SCAN
rs184580	NRG4	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76325600-76328600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr15:76326400-76328400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr15:76326600-76327800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr15:76326600-76328000	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr15:76326600-76328400	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr15:76326600-76328600	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr15:76326800-76328600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr15:76327400-76327800	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr15:76327400-76327800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr15:76327400-76328200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr15:76327400-76328200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr15:76327400-76328400	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr15:76327400-76328600	Enhancers	H1 Cell Line	embryonic stem cell
14	chr15:76327400-76328800	Enhancers	HUES64 Cell Line	embryonic stem cell

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