Variant report

Variant	rs985849
Chromosome Location	chr15:76261993-76261994
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs12910576	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12915012	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1391894	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1695378	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1699263	0.92[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs184580	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs189197	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2255701	0.93[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2441929	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2455899	0.93[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2460798	0.93[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2460800	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2469039	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2593277	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2593278	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2593280	1.00[ASW][hapmap];0.93[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28876229	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2955733	0.92[GIH][hapmap]
rs2959842	0.92[GIH][hapmap]
rs2959852	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs334930	1.00[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];0.92[GIH][hapmap];0.92[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs334934	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs334936	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs335681	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs335697	0.93[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs335706	0.91[CEU][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs335711	0.93[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4886747	0.81[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes]
rs4886753	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];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4886754	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71403522	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8024155	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv1053717	chr15:76196674-76314542	Weak transcription Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1040053	chr15:76197988-76314542	Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	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
5	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
6	nsv1042140	chr15:76243040-76298555	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv542437	chr15:76243040-76298555	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv518214	chr15:76260430-76283942	Enhancers Weak transcription Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs985849	LRRC49	cis	cerebellum	SCAN
rs985849	NRG4	cis	parietal	SCAN
rs985849	NRG4	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76249800-76262800	Weak transcription	Gastric	stomach
2	chr15:76257400-76262800	Weak transcription	Pancreas	Pancrea
3	chr15:76259000-76263200	Weak transcription	Hela-S3	cervix

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