Variant report

Variant	rs7612219
Chromosome Location	chr3:47781166-47781167
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	chr3:47781011..47782804-chr3:47820824..47822711,2	K562	blood:
2	chr3:47780810..47784890-chr3:47822002..47824979,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000173473	Chromatin interaction

Extended variants
information (count: 148 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:144)

rs_ID	r²[population]
rs1061003	0.82[AFR][1000 genomes]
rs10865948	0.86[AMR][1000 genomes]
rs11130138	0.82[AMR][1000 genomes]
rs11130143	0.90[AMR][1000 genomes]
rs11130144	0.90[AMR][1000 genomes]
rs11130145	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11130146	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11130147	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11130148	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11130150	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11707707	0.88[EUR][1000 genomes]
rs11708849	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11710199	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs11712152	0.82[EUR][1000 genomes]
rs11712464	0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11714942	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11716582	0.87[AMR][1000 genomes]
rs11927129	0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12492915	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12495204	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12497921	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs12498027	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12633604	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12635438	0.92[EUR][1000 genomes]
rs12636863	0.90[AMR][1000 genomes]
rs13061412	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13063042	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13064183	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13070035	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13077230	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13079407	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs13081356	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13084555	0.81[AMR][1000 genomes]
rs13086149	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13091913	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13094264	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13098128	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13319205	0.82[EUR][1000 genomes]
rs1403578	0.92[AMR][1000 genomes]
rs1403579	0.92[AMR][1000 genomes]
rs1464614	0.90[AMR][1000 genomes]
rs1486915	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1684942	0.81[AFR][1000 genomes]
rs17079785	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17290490	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2030596	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2047559	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2049301	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2101398	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2133601	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2140335	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2293226	0.87[AMR][1000 genomes]
rs2351248	0.84[ASN][1000 genomes]
rs2631721	0.81[AFR][1000 genomes]
rs2882611	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs319680	0.81[AFR][1000 genomes]
rs319682	0.80[AFR][1000 genomes]
rs319684	0.80[AFR][1000 genomes]
rs319687	0.82[AFR][1000 genomes]
rs319689	0.82[AFR][1000 genomes]
rs319690	0.80[AFR][1000 genomes]
rs319693	0.81[EUR][1000 genomes]
rs319694	0.84[AFR][1000 genomes]
rs34351471	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34569417	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34777284	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34906469	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35148469	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35582375	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35664069	0.89[EUR][1000 genomes]
rs35698005	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3755637	0.83[AMR][1000 genomes]
rs3755638	0.86[AMR][1000 genomes]
rs3772399	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3772403	0.86[AMR][1000 genomes]
rs3888	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3915654	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4274776	0.85[AMR][1000 genomes]
rs4410463	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4858801	0.87[AMR][1000 genomes]
rs4858803	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4858836	0.82[AMR][1000 genomes]
rs4858842	0.92[AMR][1000 genomes]
rs4858846	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4858851	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4858853	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4858857	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4858860	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4858863	0.88[EUR][1000 genomes]
rs55823596	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56376646	0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56746603	0.84[AMR][1000 genomes]
rs60110914	0.83[AMR][1000 genomes]
rs61181421	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61620099	0.87[AMR][1000 genomes]
rs62262129	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62263561	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62263575	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6442072	0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6442074	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6442079	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6442081	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6442082	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6442083	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6442085	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6442086	0.91[EUR][1000 genomes]
rs6768699	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6772301	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6773467	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6773732	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6774170	0.91[AMR][1000 genomes]
rs6776963	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6777632	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6782998	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6785031	0.82[AMR][1000 genomes]
rs6785669	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6786001	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6792350	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6792497	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6792737	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6806860	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72906474	0.82[ASN][1000 genomes]
rs72906488	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73085151	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7429162	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7613934	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7618758	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7621236	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7624474	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7629850	0.88[EUR][1000 genomes]
rs7631950	0.87[AMR][1000 genomes]
rs7637372	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7637950	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7638103	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7645846	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7646982	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7649393	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs800762	0.81[AFR][1000 genomes]
rs868255	0.92[AMR][1000 genomes]
rs870622	0.92[AMR][1000 genomes]
rs883661	0.92[AMR][1000 genomes]
rs883663	0.88[AMR][1000 genomes]
rs9757517	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9850154	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7612219	MRPS18AP1	cis	Nerve Tibial	GTEx
rs7612219	MRPS18AP1	cis	lung	GTEx
rs7612219	DHX30	Cis_1M	lymphoblastoid	RTeQTL
rs7612219	ZNF589	cis	Nerve Tibial	GTEx
rs7612219	MAP4	Cis_1M	lymphoblastoid	RTeQTL
rs7612219	MRPS18AP1	cis	Muscle Skeletal	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47656600-47790800	Strong transcription	Fetal Thymus	thymus
2	chr3:47701600-47800400	Strong transcription	Dnd41	blood
3	chr3:47701600-47819800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr3:47702200-47790400	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr3:47704000-47788600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr3:47707200-47781400	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr3:47727600-47819400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:47748400-47790600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr3:47757200-47784600	Weak transcription	Right Atrium	heart
10	chr3:47765800-47789400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr3:47766000-47781600	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr3:47766200-47788600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr3:47768200-47781600	Strong transcription	K562	blood
14	chr3:47769200-47781200	Strong transcription	Placenta	Placenta
15	chr3:47769600-47812400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr3:47769800-47817800	Weak transcription	Pancreas	Pancrea
17	chr3:47772800-47784400	Weak transcription	Fetal Heart	heart
18	chr3:47772800-47821000	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr3:47773600-47789800	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr3:47774000-47781200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr3:47774200-47792600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr3:47774200-47799000	Weak transcription	NHEK	skin
23	chr3:47774200-47820600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr3:47775200-47781600	Strong transcription	GM12878-XiMat	blood
25	chr3:47777000-47783400	Weak transcription	Stomach Mucosa	stomach
26	chr3:47777000-47786000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr3:47777000-47817600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr3:47777200-47785400	Weak transcription	Fetal Brain Female	brain
29	chr3:47777200-47794000	Weak transcription	Psoas Muscle	Psoas
30	chr3:47777200-47801400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr3:47777200-47805200	Weak transcription	Esophagus	oesophagus
32	chr3:47777200-47812400	Weak transcription	Brain Hippocampus Middle	brain
33	chr3:47777200-47813600	Weak transcription	A549	lung
34	chr3:47777200-47819000	Weak transcription	Fetal Brain Male	brain
35	chr3:47777200-47819800	Weak transcription	Small Intestine	intestine
36	chr3:47777400-47783200	Weak transcription	Left Ventricle	heart
37	chr3:47777400-47784200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr3:47777400-47784200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr3:47777400-47784400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr3:47777400-47784400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr3:47777400-47785200	Weak transcription	HSMMtube	muscle
42	chr3:47777400-47786000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr3:47777400-47786000	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr3:47777400-47786200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr3:47777400-47786600	Weak transcription	Brain Angular Gyrus	brain
46	chr3:47777400-47799600	Weak transcription	Spleen	Spleen
47	chr3:47777400-47802000	Weak transcription	Aorta	Aorta
48	chr3:47777400-47805400	Weak transcription	Gastric	stomach
49	chr3:47777400-47805600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr3:47777400-47812600	Weak transcription	Colon Smooth Muscle	Colon

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