Variant report

Variant	rs6442079
Chromosome Location	chr3:47762534-47762535
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:47762182..47765006-chr3:47770740..47772875,2	K562	blood:

Extended variants
information (count: 127 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:122)

rs_ID	r²[population]
rs10865948	0.82[AMR][1000 genomes]
rs11130143	0.83[AMR][1000 genomes]
rs11130144	0.81[AMR][1000 genomes]
rs11130145	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11130146	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11130147	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11130148	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11130150	0.84[EUR][1000 genomes]
rs11707707	0.89[EUR][1000 genomes]
rs11708849	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11710199	0.81[EUR][1000 genomes]
rs11712152	0.83[EUR][1000 genomes]
rs11712464	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11714942	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11716582	0.81[AMR][1000 genomes]
rs11927129	0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12492915	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12495204	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12497921	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12498027	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12633604	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12635438	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12636863	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs13061412	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13063042	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13064183	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13070035	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13077230	0.84[EUR][1000 genomes]
rs13081356	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13086149	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13091913	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13094264	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13098128	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13319205	0.81[EUR][1000 genomes]
rs1403578	0.83[AMR][1000 genomes]
rs1403579	0.83[AMR][1000 genomes]
rs1464614	0.83[AMR][1000 genomes]
rs1486915	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17079785	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17290490	0.80[EUR][1000 genomes]
rs2030596	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2047559	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2049301	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2101398	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2133601	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2140335	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2293226	0.81[AMR][1000 genomes]
rs2882611	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs319693	0.80[EUR][1000 genomes]
rs34351471	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34569417	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34777284	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34906469	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35148469	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35582375	0.84[EUR][1000 genomes]
rs35664069	0.91[EUR][1000 genomes]
rs35698005	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3755637	0.83[AMR][1000 genomes]
rs3772399	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3888	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3915654	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4410463	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4858801	0.81[AMR][1000 genomes]
rs4858803	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4858842	0.83[AMR][1000 genomes]
rs4858846	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4858851	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858853	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4858857	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4858860	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4858863	0.87[EUR][1000 genomes]
rs55823596	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56376646	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60110914	0.81[AMR][1000 genomes]
rs61181421	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61620099	0.81[AMR][1000 genomes]
rs62262129	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62263561	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62263575	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6442072	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6442074	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6442081	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6442082	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6442083	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6442085	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6442086	0.90[EUR][1000 genomes]
rs6768699	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6772301	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6773467	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6773732	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6774170	0.82[AMR][1000 genomes]
rs6776963	0.92[EUR][1000 genomes]
rs6777632	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6782998	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6785669	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6786001	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6792350	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6792497	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6792737	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6806860	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72906488	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73085151	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7429162	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7612219	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7613934	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7618758	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7621236	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7624474	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7629850	0.87[EUR][1000 genomes]
rs7631950	0.81[AMR][1000 genomes]
rs7637372	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7637950	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7638103	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7645846	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7646982	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7649393	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs868255	0.83[AMR][1000 genomes]
rs870622	0.83[AMR][1000 genomes]
rs883661	0.83[AMR][1000 genomes]
rs883663	0.86[AMR][1000 genomes]
rs9757517	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9850154	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv590232	chr3:47681881-47765547	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6442079	ZNF589	cis	Nerve Tibial	GTEx
rs6442079	MRPS18AP1	cis	Muscle Skeletal	GTEx
rs6442079	MRPS18AP1	cis	lung	GTEx
rs6442079	DHX30	Cis_1M	lymphoblastoid	RTeQTL
rs6442079	MAP4	Cis_1M	lymphoblastoid	RTeQTL
rs6442079	MRPS18AP1	cis	Nerve Tibial	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47655800-47765600	Strong transcription	HUES48 Cell Line	embryonic stem cell
2	chr3:47656600-47790800	Strong transcription	Fetal Thymus	thymus
3	chr3:47688200-47763400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr3:47701200-47765000	Strong transcription	HUES6 Cell Line	embryonic stem cell
5	chr3:47701200-47765600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
6	chr3:47701600-47800400	Strong transcription	Dnd41	blood
7	chr3:47701600-47819800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr3:47702200-47790400	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr3:47704000-47788600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr3:47707200-47780800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
11	chr3:47707200-47781400	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr3:47707600-47762600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr3:47723400-47766200	Strong transcription	Primary T helper cells PMA-I stimulated	--
14	chr3:47727600-47819400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:47728800-47762800	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr3:47738000-47772600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr3:47738200-47762800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr3:47738200-47779600	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr3:47738400-47766800	Strong transcription	Primary B cells from peripheral blood	blood
20	chr3:47740000-47762800	Strong transcription	H1 Cell Line	embryonic stem cell
21	chr3:47740200-47763400	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr3:47741800-47763000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr3:47742000-47762600	Strong transcription	Fetal Intestine Large	intestine
24	chr3:47742000-47779600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr3:47744000-47764200	Weak transcription	Stomach Mucosa	stomach
26	chr3:47744400-47776800	Weak transcription	Esophagus	oesophagus
27	chr3:47746000-47779200	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr3:47746200-47764400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr3:47746200-47766400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr3:47746200-47773800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr3:47747200-47772400	Weak transcription	Brain Substantia Nigra	brain
32	chr3:47748400-47790600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr3:47748800-47767800	Weak transcription	Fetal Brain Male	brain
34	chr3:47752200-47768000	Weak transcription	Small Intestine	intestine
35	chr3:47752800-47770800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr3:47753200-47775400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr3:47754400-47766000	Weak transcription	Colon Smooth Muscle	Colon
38	chr3:47755600-47767800	Weak transcription	HMEC	breast
39	chr3:47755600-47770000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr3:47755600-47772400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr3:47755600-47775600	Weak transcription	Brain Cingulate Gyrus	brain
42	chr3:47755800-47765400	Weak transcription	NHEK	skin
43	chr3:47755800-47768600	Weak transcription	Rectal Smooth Muscle	rectum
44	chr3:47755800-47774400	Weak transcription	Colonic Mucosa	Colon
45	chr3:47755800-47776200	Weak transcription	Aorta	Aorta
46	chr3:47756000-47775600	Weak transcription	Brain Angular Gyrus	brain
47	chr3:47757000-47765600	Weak transcription	Fetal Kidney	kidney
48	chr3:47757200-47776200	Weak transcription	Brain Hippocampus Middle	brain
49	chr3:47757200-47784600	Weak transcription	Right Atrium	heart
50	chr3:47757600-47764200	Weak transcription	Placenta Amnion	Placenta Amnion

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