Variant report

Variant	rs4416733
Chromosome Location	chr7:3371961-3371962
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 128 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10224159	0.81[CHB][hapmap]
rs10232765	0.81[CHB][hapmap]
rs10235815	0.81[CHB][hapmap]
rs10239408	0.92[CEU][hapmap];0.84[GIH][hapmap];0.81[TSI][hapmap]
rs10249981	0.92[CEU][hapmap]
rs10255825	0.82[EUR][1000 genomes]
rs10262464	0.81[CHB][hapmap]
rs10263832	0.80[EUR][1000 genomes]
rs10266085	0.82[EUR][1000 genomes]
rs10269416	0.82[EUR][1000 genomes]
rs10270365	0.80[CHB][hapmap]
rs10274465	0.96[CEU][hapmap];0.84[GIH][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap]
rs10277545	0.81[CHB][hapmap]
rs10278205	0.81[CHB][hapmap]
rs10281401	0.81[CHB][hapmap]
rs10435012	0.82[EUR][1000 genomes]
rs10435013	0.80[EUR][1000 genomes]
rs10435014	0.82[EUR][1000 genomes]
rs10435102	0.82[EUR][1000 genomes]
rs10435104	0.80[EUR][1000 genomes]
rs10454314	0.81[CHB][hapmap]
rs10499327	0.81[CHB][hapmap]
rs10807839	0.86[CHB][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs10951151	0.82[EUR][1000 genomes]
rs10951153	0.82[ASN][1000 genomes]
rs10951155	0.88[TSI][hapmap]
rs10951170	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11761186	0.81[CHB][hapmap]
rs11764387	0.83[CEU][hapmap];0.81[CHB][hapmap];0.81[EUR][1000 genomes]
rs11770807	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11771359	0.81[CHB][hapmap]
rs11771755	0.82[EUR][1000 genomes]
rs11979128	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11979842	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11981092	0.81[CHB][hapmap]
rs12532848	0.81[CHB][hapmap];0.89[CHD][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs12535065	0.81[CHB][hapmap];0.87[JPT][hapmap];0.80[ASN][1000 genomes]
rs12535505	0.96[ASN][1000 genomes]
rs12537325	0.99[ASN][1000 genomes]
rs12537420	0.81[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs12540385	0.99[ASN][1000 genomes]
rs12666381	0.83[EUR][1000 genomes]
rs12667184	0.81[CHB][hapmap]
rs12700808	0.94[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.84[CHD][hapmap];0.90[GIH][hapmap];0.82[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12700827	0.81[CHB][hapmap]
rs1403159	0.83[CEU][hapmap];0.80[CHB][hapmap]
rs1404873	0.82[ASN][1000 genomes]
rs1525557	0.82[CHB][hapmap]
rs1554497	0.81[CHB][hapmap]
rs1554498	0.81[CHB][hapmap]
rs1554502	0.81[CHB][hapmap]
rs1581564	0.82[EUR][1000 genomes]
rs1818931	0.82[EUR][1000 genomes]
rs1915983	0.81[CHB][hapmap]
rs2056476	0.91[CEU][hapmap]
rs2140114	0.81[CHB][hapmap]
rs34170704	0.82[EUR][1000 genomes]
rs34825038	0.82[ASN][1000 genomes]
rs35154693	0.95[ASN][1000 genomes]
rs35467252	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35682547	0.82[EUR][1000 genomes]
rs35785661	0.99[ASN][1000 genomes]
rs4236323	0.86[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs4236326	0.81[CHB][hapmap]
rs4286835	0.81[CHB][hapmap]
rs4311565	0.96[ASN][1000 genomes]
rs4343998	0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs4380820	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4391325	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4493813	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4722667	0.83[ASN][1000 genomes]
rs4722679	0.91[CHB][hapmap];0.83[ASN][1000 genomes]
rs4722695	0.84[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs4722705	0.95[CEU][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4722711	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4722713	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4722714	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4722715	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4722735	0.81[CHB][hapmap]
rs6461984	0.87[JPT][hapmap]
rs6462040	0.81[CHB][hapmap]
rs6462068	0.81[CHB][hapmap]
rs6462071	0.81[CHB][hapmap]
rs6946678	0.81[CHB][hapmap]
rs6968665	0.81[CHB][hapmap]
rs6978391	0.96[CEU][hapmap];0.81[CHB][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73046607	0.83[ASN][1000 genomes]
rs73046641	0.83[ASN][1000 genomes]
rs7457935	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7776539	0.82[EUR][1000 genomes]
rs7776559	0.94[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7777327	0.82[EUR][1000 genomes]
rs7780498	0.94[ASW][hapmap];0.88[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7783666	0.82[EUR][1000 genomes]
rs7784336	0.96[ASN][1000 genomes]
rs7784497	0.81[CHB][hapmap]
rs7785195	0.82[EUR][1000 genomes]
rs7794534	0.81[CHB][hapmap]
rs7795899	0.82[EUR][1000 genomes]
rs7798141	0.81[CHB][hapmap]
rs7799953	0.82[EUR][1000 genomes]
rs7800260	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs939912	0.81[CHB][hapmap]
rs9654984	0.82[EUR][1000 genomes]
rs9655268	0.80[EUR][1000 genomes]
rs9655269	0.85[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023127	chr7:3216344-3466223	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv1018173	chr7:3258989-3879848	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv538660	chr7:3258989-3879848	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv2758100	chr7:3286625-3560229	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	esv2759500	chr7:3286625-3560229	Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1016555	chr7:3298478-3872512	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv538661	chr7:3298478-3872512	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1019515	chr7:3300048-3479972	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv887324	chr7:3308195-3400105	Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv605892	chr7:3341589-3424878	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv1020764	chr7:3348458-3554820	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv538662	chr7:3348458-3554820	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv1019492	chr7:3359294-3479972	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	nsv538663	chr7:3359294-3479972	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
15	esv2757204	chr7:3359491-3460355	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
16	nsv1028585	chr7:3364990-3400105	Enhancers Weak transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
17	nsv1030484	chr7:3364990-3506102	Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
18	esv2764026	chr7:3365002-3618361	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
19	nsv1018105	chr7:3365441-3506102	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
20	nsv1026361	chr7:3366960-3502600	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
21	nsv538664	chr7:3366960-3502600	Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
22	nsv605893	chr7:3368197-3505231	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4416733	LOC389458	cis	cerebellum	SCAN
rs4416733	KDELR2	cis	parietal	SCAN
rs4416733	C7orf50	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:3359000-3385800	Weak transcription	Pancreas	Pancrea
2	chr7:3363400-3377800	Weak transcription	Aorta	Aorta
3	chr7:3366800-3372600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr7:3367800-3373000	Weak transcription	Pancreatic Islets	Pancreatic Islet

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