Variant report

Variant	rs6442086
Chromosome Location	chr3:47824983-47824984
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:47809506..47818715-chr3:47820075..47824996,15	MCF-7	breast:
2	chr3:47555041..47556961-chr3:47821638..47825112,3	MCF-7	breast:
3	chr3:47821496..47825290-chr3:47843622..47845759,4	MCF-7	breast:
4	chr3:47582862..47584388-chr3:47823797..47825986,2	K562	blood:
5	chr3:47819738..47825460-chr3:47843094..47847845,6	K562	blood:
6	chr3:47756501..47758840-chr3:47823699..47825291,2	K562	blood:
7	chr3:47775553..47777861-chr3:47823812..47825481,2	K562	blood:
8	chr3:47617723..47621182-chr3:47821900..47825077,3	MCF-7	breast:
9	chr3:47787198..47789332-chr3:47822441..47824997,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000114646	Chromatin interaction
ENSG00000163832	Chromatin interaction
ENSG00000173473	Chromatin interaction
ENSG00000266457	Chromatin interaction
ENSG00000132153	Chromatin interaction

Extended variants
information (count: 100 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs11130147	0.90[EUR][1000 genomes]
rs11130148	0.90[EUR][1000 genomes]
rs11130150	0.88[EUR][1000 genomes]
rs11707707	0.92[AMR][1000 genomes]
rs11708849	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11710199	0.85[EUR][1000 genomes]
rs11712152	0.94[AMR][1000 genomes]
rs11712464	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11714942	0.87[EUR][1000 genomes]
rs11927129	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11929303	0.88[AMR][1000 genomes]
rs12495204	0.90[EUR][1000 genomes]
rs12635438	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12636198	0.88[AMR][1000 genomes]
rs13063042	0.81[EUR][1000 genomes]
rs13064183	0.90[EUR][1000 genomes]
rs13069142	0.84[AMR][1000 genomes]
rs13070035	0.88[EUR][1000 genomes]
rs13077230	0.88[EUR][1000 genomes]
rs13079407	0.85[EUR][1000 genomes]
rs13085978	0.89[AMR][1000 genomes]
rs13086149	0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13091913	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13094264	0.90[EUR][1000 genomes]
rs13098128	0.93[EUR][1000 genomes]
rs1486915	0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17079785	0.91[EUR][1000 genomes]
rs17290490	0.84[EUR][1000 genomes]
rs2030596	0.83[EUR][1000 genomes]
rs2047559	0.83[EUR][1000 genomes]
rs2049301	0.81[EUR][1000 genomes]
rs2101398	0.91[EUR][1000 genomes]
rs2133601	0.82[EUR][1000 genomes]
rs319693	0.84[EUR][1000 genomes]
rs34351471	0.88[EUR][1000 genomes]
rs34569417	0.93[EUR][1000 genomes]
rs34777284	0.89[EUR][1000 genomes]
rs34906469	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35148469	0.91[EUR][1000 genomes]
rs35167544	0.84[AMR][1000 genomes]
rs35582375	0.88[EUR][1000 genomes]
rs35664069	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35698005	0.96[EUR][1000 genomes]
rs3772399	0.91[EUR][1000 genomes]
rs3888	0.93[EUR][1000 genomes]
rs3915654	0.91[EUR][1000 genomes]
rs4410463	0.83[EUR][1000 genomes]
rs4858851	0.89[EUR][1000 genomes]
rs4858853	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4858857	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4858860	0.93[EUR][1000 genomes]
rs4858863	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55823596	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56376646	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61181421	0.96[EUR][1000 genomes]
rs61675361	0.86[AMR][1000 genomes]
rs62262129	0.82[EUR][1000 genomes]
rs62263561	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62263575	0.91[EUR][1000 genomes]
rs6442079	0.90[EUR][1000 genomes]
rs6442081	0.90[EUR][1000 genomes]
rs6442082	0.91[EUR][1000 genomes]
rs6442083	0.90[EUR][1000 genomes]
rs6442085	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6768699	0.90[EUR][1000 genomes]
rs6772301	0.81[EUR][1000 genomes]
rs6773467	0.81[EUR][1000 genomes]
rs6773732	0.81[EUR][1000 genomes]
rs6776963	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6777632	0.93[EUR][1000 genomes]
rs6782998	0.82[EUR][1000 genomes]
rs6785669	0.89[EUR][1000 genomes]
rs6786001	0.90[EUR][1000 genomes]
rs6792350	0.97[EUR][1000 genomes]
rs6792497	0.83[EUR][1000 genomes]
rs6792737	0.86[EUR][1000 genomes]
rs6806860	0.90[EUR][1000 genomes]
rs72906488	0.96[EUR][1000 genomes]
rs73085151	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7429162	0.81[EUR][1000 genomes]
rs7612219	0.91[EUR][1000 genomes]
rs7618758	0.90[EUR][1000 genomes]
rs7629850	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7637372	0.93[EUR][1000 genomes]
rs7637950	0.93[EUR][1000 genomes]
rs7638103	0.90[EUR][1000 genomes]
rs7645846	0.90[EUR][1000 genomes]
rs7646982	0.84[EUR][1000 genomes]
rs7649393	0.90[EUR][1000 genomes]
rs869508	0.88[AMR][1000 genomes]
rs883662	0.89[AMR][1000 genomes]
rs9757517	0.93[EUR][1000 genomes]
rs9850154	0.85[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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs6442086	DHX30	Cis_1M	lymphoblastoid	RTeQTL
rs6442086	NME6	cis	Esophagus Muscularis	GTEx
rs6442086	ZNF589	cis	Nerve Tibial	GTEx
rs6442086	MRPS18AP1	cis	Nerve Tibial	GTEx
rs6442086	MRPS18AP1	cis	Muscle Skeletal	GTEx
rs6442086	MRPS18AP1	cis	Artery Tibial	GTEx
rs6442086	MAP4	Cis_1M	lymphoblastoid	RTeQTL
rs6442086	ZNF589	cis	Whole Blood	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47820000-47825200	Active TSS	GM12878-XiMat	blood
2	chr3:47824000-47825000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:47824000-47825000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:47824200-47825000	Enhancers	Placenta Amnion	Placenta Amnion
5	chr3:47824200-47825000	Active TSS	HepG2	liver
6	chr3:47824600-47825000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr3:47824600-47825000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr3:47824600-47825200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr3:47824600-47825400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr3:47824600-47826800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr3:47824600-47829800	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr3:47824600-47829800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr3:47824600-47830000	Weak transcription	Primary B cells from cord blood	blood
14	chr3:47824600-47830000	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr3:47824600-47830000	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr3:47824600-47830000	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr3:47824600-47830200	Weak transcription	Right Atrium	heart
18	chr3:47824600-47830400	Weak transcription	Stomach Mucosa	stomach
19	chr3:47824800-47825800	Enhancers	K562	blood
20	chr3:47824800-47829800	Weak transcription	Primary B cells from peripheral blood	blood
21	chr3:47824800-47829800	Weak transcription	Dnd41	blood

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