Variant report

Variant	rs2351248
Chromosome Location	chr3:47829277-47829278
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:47562617..47565330-chr3:47829264..47832654,4	MCF-7	breast:
2	chr3:47827524..47829723-chr3:47850586..47853080,2	K562	blood:
3	chr3:47821493..47825300-chr3:47828979..47831183,6	K562	blood:
4	chr3:47513969..47516839-chr3:47829270..47830805,2	K562	blood:

Variant related genes	Relation type
ENSG00000173473	Chromatin interaction

Extended variants
information (count: 105 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs1013431	0.80[CEU][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap]
rs1014228	0.85[CEU][hapmap];0.85[GIH][hapmap];0.84[TSI][hapmap]
rs1060407	0.82[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.97[TSI][hapmap]
rs11130143	0.82[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap]
rs11130144	0.84[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap]
rs11130146	0.82[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap]
rs11130147	0.81[ASN][1000 genomes]
rs11130148	0.82[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.81[ASN][1000 genomes]
rs11707679	0.82[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.97[TSI][hapmap]
rs11708849	0.87[ASN][1000 genomes]
rs11712464	0.82[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.94[TSI][hapmap]
rs11714942	0.84[ASN][1000 genomes]
rs11716582	0.82[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap]
rs12495204	0.91[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap]
rs12635438	0.82[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.89[TSI][hapmap]
rs13061412	0.82[CEU][hapmap]
rs13063042	0.82[CEU][hapmap];0.84[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap]
rs13064183	0.84[ASN][1000 genomes]
rs13074973	0.80[CEU][hapmap];1.00[JPT][hapmap]
rs13079407	0.87[CEU][hapmap]
rs13086149	0.90[ASN][1000 genomes]
rs13091913	0.81[CEU][hapmap];0.84[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.86[ASN][1000 genomes]
rs13094264	0.81[CEU][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap]
rs13098128	0.84[ASN][1000 genomes]
rs1403578	0.82[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap]
rs1403579	0.82[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap]
rs1464614	0.82[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap]
rs1486915	0.81[CEU][hapmap];0.84[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.88[ASN][1000 genomes]
rs1684942	1.00[JPT][hapmap]
rs17079785	0.82[CEU][hapmap];0.84[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.84[ASN][1000 genomes]
rs17290490	0.82[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap]
rs2047559	0.82[CEU][hapmap]
rs2133601	0.86[CHD][hapmap];0.83[GIH][hapmap];0.82[TSI][hapmap]
rs2140335	0.81[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap]
rs2166770	0.80[CEU][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap]
rs2882611	0.81[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs319682	1.00[JPT][hapmap];0.97[TSI][hapmap]
rs319693	0.82[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.94[TSI][hapmap]
rs319694	0.84[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.83[TSI][hapmap]
rs319695	0.88[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap]
rs319696	1.00[JPT][hapmap]
rs34777284	0.81[ASN][1000 genomes]
rs34906469	0.90[ASN][1000 genomes]
rs35148469	0.84[ASN][1000 genomes]
rs35698005	0.84[ASN][1000 genomes]
rs3772399	0.82[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap]
rs3888	0.82[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap]
rs3915654	0.82[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap]
rs4274776	0.82[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap]
rs4858801	0.81[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs4858842	0.82[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap]
rs4858846	0.81[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap]
rs4858851	0.82[CEU][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap]
rs4858857	0.86[ASN][1000 genomes]
rs4858860	0.82[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap]
rs4858863	0.82[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.94[TSI][hapmap]
rs4858871	1.00[JPT][hapmap];0.97[TSI][hapmap]
rs61181421	0.86[ASN][1000 genomes]
rs6442081	0.81[ASN][1000 genomes]
rs6442082	0.81[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.84[ASN][1000 genomes]
rs6442083	0.84[ASN][1000 genomes]
rs6442085	0.81[ASN][1000 genomes]
rs6768699	0.82[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap]
rs6772301	0.84[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap]
rs6774170	0.85[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap]
rs6776963	0.88[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.94[TSI][hapmap]
rs6777632	0.81[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6785669	0.84[CEU][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.81[ASN][1000 genomes]
rs6786001	0.82[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.81[ASN][1000 genomes]
rs6792350	0.84[ASN][1000 genomes]
rs6792497	0.82[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap]
rs6792737	0.82[ASN][1000 genomes]
rs6806860	0.84[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap]
rs72906488	0.84[ASN][1000 genomes]
rs7374516	0.80[CEU][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap]
rs7426976	0.84[CHB][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap]
rs7427418	0.84[CHB][hapmap];0.84[JPT][hapmap];0.92[TSI][hapmap]
rs7429162	0.82[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap]
rs7612219	0.84[ASN][1000 genomes]
rs7613934	0.82[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap]
rs7618758	0.82[CEU][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap]
rs7621236	0.82[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap]
rs7624474	0.82[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap]
rs7629850	0.82[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.94[TSI][hapmap]
rs7631950	0.82[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap]
rs7637372	0.83[ASN][1000 genomes]
rs7637950	0.83[ASN][1000 genomes]
rs7638103	0.82[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.81[ASN][1000 genomes]
rs7645846	0.85[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7649393	0.81[ASN][1000 genomes]
rs777015	1.00[JPT][hapmap];0.97[TSI][hapmap]
rs810334	1.00[JPT][hapmap];0.97[TSI][hapmap]
rs870622	0.87[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs883662	0.81[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap]
rs883663	0.82[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap]
rs9681917	0.82[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap]
rs9757517	0.86[ASN][1000 genomes]
rs9862913	0.80[CEU][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap]

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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2351248	MRPS18AP1	cis	Muscle Skeletal	GTEx
rs2351248	NME6	cis	Esophagus Muscularis	GTEx
rs2351248	DHX30	Cis_1M	lymphoblastoid	RTeQTL
rs2351248	ZNF589	cis	Nerve Tibial	GTEx
rs2351248	MAP4	Cis_1M	lymphoblastoid	RTeQTL
rs2351248	MRPS18AP1	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47824600-47829800	Weak transcription	Primary monocytes fromperipheralblood	blood
2	chr3:47824600-47829800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr3:47824600-47830000	Weak transcription	Primary B cells from cord blood	blood
4	chr3:47824600-47830000	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr3:47824600-47830000	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr3:47824600-47830000	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr3:47824600-47830200	Weak transcription	Right Atrium	heart
8	chr3:47824600-47830400	Weak transcription	Stomach Mucosa	stomach
9	chr3:47824800-47829800	Weak transcription	Primary B cells from peripheral blood	blood
10	chr3:47824800-47829800	Weak transcription	Dnd41	blood
11	chr3:47825000-47829800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr3:47825000-47830000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr3:47825600-47830200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr3:47825800-47829800	Weak transcription	K562	blood
15	chr3:47828000-47830400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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