Variant report

Variant	rs10039253
Chromosome Location	chr5:151866663-151866664
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 223 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:220)

rs_ID	r²[population]
rs10065026	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10069107	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10072743	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10213914	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1035398	1.00[JPT][hapmap]
rs10476784	0.90[ASN][1000 genomes]
rs10515658	0.90[ASN][1000 genomes]
rs10515660	0.90[ASN][1000 genomes]
rs10515661	0.90[ASN][1000 genomes]
rs10515662	0.90[ASN][1000 genomes]
rs10515663	0.90[ASN][1000 genomes]
rs10515664	0.90[ASN][1000 genomes]
rs10515665	0.90[ASN][1000 genomes]
rs10515667	0.90[ASN][1000 genomes]
rs10515669	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10515670	0.90[ASN][1000 genomes]
rs10515671	0.90[ASN][1000 genomes]
rs1156932	0.90[ASN][1000 genomes]
rs1156933	0.90[ASN][1000 genomes]
rs1319549	0.90[ASN][1000 genomes]
rs13354964	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13357099	0.90[AFR][1000 genomes]
rs13361745	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1363407	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1363408	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1363409	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1363413	0.82[ASN][1000 genomes]
rs1363420	0.90[ASN][1000 genomes]
rs1363421	0.90[ASN][1000 genomes]
rs1422340	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1422341	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1422342	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1422343	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1422344	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1422356	0.90[ASN][1000 genomes]
rs1422357	0.90[ASN][1000 genomes]
rs1422371	0.90[ASN][1000 genomes]
rs1541651	0.90[ASN][1000 genomes]
rs1541652	0.90[ASN][1000 genomes]
rs1541653	0.90[ASN][1000 genomes]
rs1592896	0.82[ASN][1000 genomes]
rs17113223	0.85[ASN][1000 genomes]
rs17113291	1.00[JPT][hapmap]
rs17447016	0.82[ASN][1000 genomes]
rs17448379	0.90[ASN][1000 genomes]
rs17448407	0.90[ASN][1000 genomes]
rs17448511	0.90[ASN][1000 genomes]
rs17448739	0.90[ASN][1000 genomes]
rs17448815	0.90[ASN][1000 genomes]
rs17451282	1.00[JPT][hapmap]
rs17451303	1.00[JPT][hapmap];0.89[MEX][hapmap]
rs17544525	0.81[ASN][1000 genomes]
rs17545297	0.90[ASN][1000 genomes]
rs17545332	0.90[ASN][1000 genomes]
rs17545367	0.90[ASN][1000 genomes]
rs17545665	0.90[ASN][1000 genomes]
rs17545881	0.90[ASN][1000 genomes]
rs17546335	0.90[ASN][1000 genomes]
rs17546405	0.90[ASN][1000 genomes]
rs17548153	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17548209	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17549488	1.00[JPT][hapmap]
rs1895245	0.90[ASN][1000 genomes]
rs1946224	0.90[ASN][1000 genomes]
rs1946225	0.90[ASN][1000 genomes]
rs2080929	0.90[ASN][1000 genomes]
rs2080930	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2194084	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2348421	0.90[ASN][1000 genomes]
rs2348422	0.90[ASN][1000 genomes]
rs2348425	0.90[ASN][1000 genomes]
rs2348426	0.90[ASN][1000 genomes]
rs28374977	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28495602	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28639501	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3763130	0.90[ASN][1000 genomes]
rs3792907	0.90[ASN][1000 genomes]
rs3828684	0.90[ASN][1000 genomes]
rs41290593	0.90[ASN][1000 genomes]
rs4392608	0.90[ASN][1000 genomes]
rs4958303	0.90[ASN][1000 genomes]
rs4958304	0.90[ASN][1000 genomes]
rs4958305	0.90[ASN][1000 genomes]
rs4958306	0.90[ASN][1000 genomes]
rs4958307	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4958308	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4958311	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4958312	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4958313	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4958314	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4958531	0.90[ASN][1000 genomes]
rs4958532	0.90[ASN][1000 genomes]
rs4958534	0.90[ASN][1000 genomes]
rs4958535	0.90[ASN][1000 genomes]
rs4958536	0.90[ASN][1000 genomes]
rs4958537	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[ASN][1000 genomes]
rs4958541	0.90[ASN][1000 genomes]
rs4958543	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4958544	0.90[ASN][1000 genomes]
rs4958546	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4958547	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4958548	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55687380	0.90[ASN][1000 genomes]
rs55689355	0.90[ASN][1000 genomes]
rs55696776	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55715312	0.90[ASN][1000 genomes]
rs55726523	0.86[ASN][1000 genomes]
rs55761989	0.90[ASN][1000 genomes]
rs55846431	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55893124	0.90[ASN][1000 genomes]
rs55911705	0.90[ASN][1000 genomes]
rs55917590	0.82[ASN][1000 genomes]
rs56035517	0.90[ASN][1000 genomes]
rs56035552	0.90[ASN][1000 genomes]
rs56074869	0.90[ASN][1000 genomes]
rs56091570	0.90[ASN][1000 genomes]
rs56125782	0.90[ASN][1000 genomes]
rs56211663	0.90[ASN][1000 genomes]
rs56245652	0.90[ASN][1000 genomes]
rs56275648	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56382127	0.90[ASN][1000 genomes]
rs56392306	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59365202	0.90[ASN][1000 genomes]
rs6864518	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6864702	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6884899	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6886963	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs716256	0.90[ASN][1000 genomes]
rs716257	0.90[ASN][1000 genomes]
rs72791404	0.90[ASN][1000 genomes]
rs72791406	0.90[ASN][1000 genomes]
rs72791407	0.90[ASN][1000 genomes]
rs72791408	0.90[ASN][1000 genomes]
rs72791409	0.90[ASN][1000 genomes]
rs72791410	0.90[ASN][1000 genomes]
rs72791411	0.90[ASN][1000 genomes]
rs72791413	0.90[ASN][1000 genomes]
rs72791415	0.90[ASN][1000 genomes]
rs72791419	0.90[ASN][1000 genomes]
rs72791420	0.90[ASN][1000 genomes]
rs72791421	0.90[ASN][1000 genomes]
rs72791422	0.90[ASN][1000 genomes]
rs72791423	0.90[ASN][1000 genomes]
rs72791424	0.90[ASN][1000 genomes]
rs72791425	0.90[ASN][1000 genomes]
rs72791429	0.90[ASN][1000 genomes]
rs72791432	0.90[ASN][1000 genomes]
rs72791434	0.90[ASN][1000 genomes]
rs72791435	0.90[ASN][1000 genomes]
rs72791441	0.90[ASN][1000 genomes]
rs72791442	0.90[ASN][1000 genomes]
rs72791445	0.90[ASN][1000 genomes]
rs72791446	0.90[ASN][1000 genomes]
rs72791447	0.90[ASN][1000 genomes]
rs72791449	0.90[ASN][1000 genomes]
rs72791451	0.90[ASN][1000 genomes]
rs72791452	0.90[ASN][1000 genomes]
rs72791454	0.90[ASN][1000 genomes]
rs72791456	0.90[ASN][1000 genomes]
rs72791458	0.90[ASN][1000 genomes]
rs72791461	0.90[ASN][1000 genomes]
rs72791463	0.90[ASN][1000 genomes]
rs72791464	0.90[ASN][1000 genomes]
rs72791468	0.90[ASN][1000 genomes]
rs72791470	0.90[ASN][1000 genomes]
rs72791475	0.90[ASN][1000 genomes]
rs72791477	0.90[ASN][1000 genomes]
rs72791485	0.90[ASN][1000 genomes]
rs72791486	0.90[ASN][1000 genomes]
rs72791488	0.90[ASN][1000 genomes]
rs72791490	0.90[ASN][1000 genomes]
rs72791492	0.90[ASN][1000 genomes]
rs72791494	0.90[ASN][1000 genomes]
rs72791495	0.90[ASN][1000 genomes]
rs72791498	0.86[ASN][1000 genomes]
rs72791499	0.90[ASN][1000 genomes]
rs72793405	0.90[ASN][1000 genomes]
rs72793406	0.90[ASN][1000 genomes]
rs72793407	0.90[ASN][1000 genomes]
rs72793408	0.90[ASN][1000 genomes]
rs72793437	0.90[ASN][1000 genomes]
rs72793438	0.90[ASN][1000 genomes]
rs72793439	0.86[ASN][1000 genomes]
rs72793455	0.90[ASN][1000 genomes]
rs72793460	0.90[ASN][1000 genomes]
rs72793462	0.90[ASN][1000 genomes]
rs72793463	0.90[ASN][1000 genomes]
rs72793466	0.90[ASN][1000 genomes]
rs72793468	0.90[ASN][1000 genomes]
rs72793469	0.90[ASN][1000 genomes]
rs72793472	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72793476	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72793480	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72793481	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72793485	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72793487	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72793488	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72793497	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72808307	0.82[ASN][1000 genomes]
rs72808310	0.82[ASN][1000 genomes]
rs72808322	0.82[ASN][1000 genomes]
rs72808324	0.82[ASN][1000 genomes]
rs72808326	0.82[ASN][1000 genomes]
rs72808328	0.82[ASN][1000 genomes]
rs72808330	0.82[ASN][1000 genomes]
rs72808338	0.82[ASN][1000 genomes]
rs72808345	0.90[ASN][1000 genomes]
rs72808347	0.85[ASN][1000 genomes]
rs72808348	0.85[ASN][1000 genomes]
rs731117	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7356769	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs766895	0.82[ASN][1000 genomes]
rs888877	0.85[ASN][1000 genomes]
rs888878	0.90[ASN][1000 genomes]
rs888879	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs957211	0.90[ASN][1000 genomes]
rs982418	0.90[ASN][1000 genomes]
rs982714	0.90[ASN][1000 genomes]
rs982715	0.90[ASN][1000 genomes]
rs982716	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[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	nsv1023828	chr5:151522149-151956217	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv432815	chr5:151682807-151875807	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv432816	chr5:151691807-151875807	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs10039253	AFAP1L1	cis	cerebellum	SCAN
rs10039253	NMUR2	cis	Thyroid	GTEx
rs10039253	SAP30L	cis	cerebellum	SCAN
rs10039253	NMUR2	cis	parietal	SCAN
rs10039253	CAMK2A	cis	cerebellum	SCAN
rs10039253	SLC36A1	cis	parietal	SCAN
rs10039253	GLRA1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:151866200-151866800	Enhancers	Brain Hippocampus Middle	brain
2	chr5:151866200-151867800	Enhancers	Brain Cingulate Gyrus	brain
3	chr5:151866400-151867000	Enhancers	Brain Anterior Caudate	brain
4	chr5:151866400-151867000	Enhancers	Brain Inferior Temporal Lobe	brain

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