Variant report

Variant	rs13086149
Chromosome Location	chr3:47825648-47825649
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CUX1	chr3:47825408-47825766	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:47582862..47584388-chr3:47823797..47825986,2	K562	blood:

Variant related genes	Relation type
SMARCC1	TF binding region

Extended variants
information (count: 157 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:150)

rs_ID	r²[population]
rs1061003	0.83[AFR][1000 genomes]
rs10865948	0.89[AMR][1000 genomes]
rs11130138	0.84[AMR][1000 genomes]
rs11130143	0.87[AMR][1000 genomes]
rs11130144	0.87[AMR][1000 genomes]
rs11130145	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs11130146	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11130147	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11130148	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11130150	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11707707	0.81[EUR][1000 genomes]
rs11708849	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11710199	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11712464	0.92[EUR][1000 genomes]
rs11714942	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11716582	0.90[AMR][1000 genomes]
rs11927129	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12492915	0.92[AMR][1000 genomes]
rs12495204	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12497921	0.92[AMR][1000 genomes]
rs12498027	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs12633604	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12635438	0.85[EUR][1000 genomes]
rs12636863	0.87[AMR][1000 genomes]
rs13061412	0.93[AMR][1000 genomes]
rs13063042	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13064183	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13070035	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13077230	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13079407	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13081356	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs13084555	0.83[AMR][1000 genomes]
rs13091913	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13094264	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13098128	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13319205	0.81[EUR][1000 genomes]
rs1403578	0.90[AMR][1000 genomes]
rs1403579	0.90[AMR][1000 genomes]
rs1464614	0.87[AMR][1000 genomes]
rs1486915	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1684942	0.83[AFR][1000 genomes]
rs17079785	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17290490	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2030596	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2047559	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2049301	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2101398	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2133601	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2140335	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2293226	0.90[AMR][1000 genomes]
rs2351248	0.90[ASN][1000 genomes]
rs2631721	0.81[AFR][1000 genomes]
rs2882611	0.90[AMR][1000 genomes]
rs319680	0.82[AFR][1000 genomes]
rs319682	0.80[AFR][1000 genomes]
rs319684	0.83[AFR][1000 genomes]
rs319685	0.82[AFR][1000 genomes]
rs319687	0.82[AFR][1000 genomes]
rs319689	0.82[AFR][1000 genomes]
rs319690	0.83[AFR][1000 genomes]
rs319691	0.82[AFR][1000 genomes]
rs319693	0.86[EUR][1000 genomes]
rs319694	0.84[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs34249203	0.80[EUR][1000 genomes]
rs34351471	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34569417	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34777284	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34906469	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35148469	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35582375	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35664069	0.83[EUR][1000 genomes]
rs35698005	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3755637	0.85[AMR][1000 genomes]
rs3755638	0.89[AMR][1000 genomes]
rs3772399	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3772403	0.89[AMR][1000 genomes]
rs3888	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3915654	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4274776	0.87[AMR][1000 genomes]
rs4410463	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4858801	0.90[AMR][1000 genomes]
rs4858803	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs4858836	0.84[AMR][1000 genomes]
rs4858842	0.90[AMR][1000 genomes]
rs4858846	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs4858851	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4858853	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4858857	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4858860	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4858863	0.95[EUR][1000 genomes]
rs55823596	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56376646	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56746603	0.86[AMR][1000 genomes]
rs60110914	0.85[AMR][1000 genomes]
rs61181421	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61620099	0.90[AMR][1000 genomes]
rs62262129	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62263561	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62263575	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6442072	0.87[AMR][1000 genomes]
rs6442074	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6442079	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6442081	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6442082	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6442083	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6442085	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6442086	0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6767896	0.81[AMR][1000 genomes]
rs6768699	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6772301	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6773467	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6773732	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6774170	0.89[AMR][1000 genomes]
rs6776963	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6777632	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6782998	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6784946	0.82[AMR][1000 genomes]
rs6785031	0.84[AMR][1000 genomes]
rs6785669	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6786001	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6792350	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6792497	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6792737	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6806860	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72906474	0.85[ASN][1000 genomes]
rs72906488	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73085151	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7429162	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7612219	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7613934	0.92[AMR][1000 genomes]
rs7618758	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7621236	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs7624474	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs7629850	0.95[EUR][1000 genomes]
rs7631950	0.90[AMR][1000 genomes]
rs7637372	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7637950	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7638103	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7645846	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7646982	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7649393	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs777015	0.81[AFR][1000 genomes]
rs800762	0.83[AFR][1000 genomes]
rs810334	0.81[AFR][1000 genomes]
rs868255	0.90[AMR][1000 genomes]
rs870622	0.90[AMR][1000 genomes]
rs883661	0.90[AMR][1000 genomes]
rs883663	0.86[AMR][1000 genomes]
rs9757517	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9850154	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003072	chr3:47673628-47869154	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	nsv876758	chr3:47681881-47842234	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases
3	nsv876759	chr3:47725315-47830741	Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	24 gene(s)	inside rSNPs	diseases
4	nsv834679	chr3:47749475-47924006	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	167 gene(s)	inside rSNPs	diseases
5	nsv590233	chr3:47798700-47829277	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases
6	nsv965333	chr3:47815622-47845296	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	nsv10270	chr3:47822606-47845578	Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs13086149	MAP4	Cis_1M	lymphoblastoid	RTeQTL
rs13086149	MRPS18AP1	cis	Nerve Tibial	GTEx
rs13086149	DHX30	Cis_1M	lymphoblastoid	RTeQTL
rs13086149	MRPS18AP1	cis	Muscle Skeletal	GTEx
rs13086149	ZNF589	cis	Nerve Tibial	GTEx

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47824600-47826800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr3:47824600-47829800	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr3:47824600-47829800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr3:47824600-47830000	Weak transcription	Primary B cells from cord blood	blood
5	chr3:47824600-47830000	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr3:47824600-47830000	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr3:47824600-47830000	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr3:47824600-47830200	Weak transcription	Right Atrium	heart
9	chr3:47824600-47830400	Weak transcription	Stomach Mucosa	stomach
10	chr3:47824800-47825800	Enhancers	K562	blood
11	chr3:47824800-47829800	Weak transcription	Primary B cells from peripheral blood	blood
12	chr3:47824800-47829800	Weak transcription	Dnd41	blood
13	chr3:47825000-47829800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr3:47825000-47830000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr3:47825600-47830200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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