Variant report

Variant	rs1376725
Chromosome Location	chr8:39537431-39537432
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10088799	0.84[ASN][1000 genomes]
rs10099250	0.81[ASN][1000 genomes]
rs10106405	0.81[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10107204	0.84[ASN][1000 genomes]
rs10108019	0.81[CHB][hapmap];0.82[CHD][hapmap];0.89[JPT][hapmap]
rs10110653	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11777357	0.82[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];0.83[YRI][hapmap]
rs11778483	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11785708	0.94[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.90[LWK][hapmap];0.91[YRI][hapmap]
rs11985352	0.91[YRI][hapmap]
rs11988623	0.82[LWK][hapmap];0.91[YRI][hapmap]
rs11991456	0.82[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12548363	0.86[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12550405	0.94[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs12550731	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12679668	0.91[YRI][hapmap]
rs13248954	0.82[LWK][hapmap];0.91[YRI][hapmap]
rs13260129	0.94[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap]
rs13276944	0.88[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap]
rs13277716	0.82[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1349545	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1349547	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1376720	0.94[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap]
rs1376726	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]
rs1451736	0.87[MEX][hapmap]
rs1901388	0.87[MEX][hapmap]
rs1993120	0.90[LWK][hapmap];0.92[MKK][hapmap];0.91[YRI][hapmap]
rs2060802	0.94[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap]
rs2100310	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2305392	0.86[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2350466	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28730314	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34113924	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34466265	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35739681	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35893648	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3735880	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3824144	0.94[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.90[LWK][hapmap];0.81[MKK][hapmap];0.91[YRI][hapmap]
rs4297011	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs4376471	0.94[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs4584120	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs4733923	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4734001	0.81[CHB][hapmap];0.89[JPT][hapmap]
rs62511904	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62511905	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6474161	0.94[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap]
rs6474162	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6980957	1.00[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap]
rs6988389	0.87[LWK][hapmap];0.92[MKK][hapmap];0.91[YRI][hapmap]
rs72641297	0.83[ASN][1000 genomes]
rs7461232	0.88[AMR][1000 genomes]
rs7463730	0.87[MEX][hapmap]
rs7820447	0.94[CHB][hapmap];0.93[JPT][hapmap];0.91[YRI][hapmap]
rs7831283	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7835711	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7837204	0.80[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap]
rs7838350	0.82[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]
rs9298571	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9643868	0.88[LWK][hapmap];0.92[MKK][hapmap];0.91[YRI][hapmap]
rs9657175	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015907	chr8:38967169-39718559	Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv539550	chr8:38967169-39718559	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	esv2759608	chr8:39174279-39597639	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv890725	chr8:39212435-39587864	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	esv2758154	chr8:39245798-39597639	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1021340	chr8:39268667-39577905	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv890830	chr8:39378400-39575853	Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv890833	chr8:39405337-39664696	Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv890834	chr8:39429071-39586358	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv890836	chr8:39480366-39650940	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv890837	chr8:39507869-39609626	Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv1017740	chr8:39511974-39586376	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv1033943	chr8:39515917-39577905	Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
14	nsv522716	chr8:39522613-39594979	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv890838	chr8:39525174-39586358	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1376725	RAB11FIP1	cis	cerebellum	SCAN
rs1376725	C8orf4	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:39534000-39542000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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