Variant report

Variant	rs62263575
Chromosome Location	chr3:47856246-47856247
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:47850679..47853675-chr3:47855656..47858435,3	K562	blood:
2	chr3:47855068..47856997-chr3:47862037..47863595,2	K562	blood:
3	chr3:47855333..47857143-chr3:47860194..47862365,2	MCF-7	breast:
4	chr3:47851691..47863624-chr3:47863694..47870558,21	K562	blood:
5	chr3:47850483..47856831-chr3:47865634..47869803,7	K562	blood:
6	chr3:47854506..47856752-chr3:47863004..47865174,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000132153	Chromatin interaction

Extended variants
information (count: 130 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:128)

rs_ID	r²[population]
rs1061003	0.87[ASN][1000 genomes]
rs10865948	0.81[AMR][1000 genomes]
rs11130145	0.85[AMR][1000 genomes]
rs11130146	0.86[AMR][1000 genomes]
rs11130147	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11130148	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11130150	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1137524	0.83[ASN][1000 genomes]
rs11708849	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11710199	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11712464	0.85[EUR][1000 genomes]
rs11714942	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11927129	0.85[EUR][1000 genomes]
rs12492915	0.82[AMR][1000 genomes]
rs12495204	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12497921	0.84[AMR][1000 genomes]
rs12498027	0.84[AMR][1000 genomes]
rs12633604	0.83[AMR][1000 genomes]
rs13061412	0.90[AMR][1000 genomes]
rs13063042	0.84[AMR][1000 genomes]
rs13064183	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13070035	0.85[EUR][1000 genomes]
rs13077230	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13079407	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13081356	0.85[AMR][1000 genomes]
rs13086149	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13091913	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13094264	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13098128	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1486915	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1684942	0.84[ASN][1000 genomes]
rs17079785	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17290490	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs184388	0.81[ASN][1000 genomes]
rs2030596	0.82[AMR][1000 genomes]
rs2047559	0.82[AMR][1000 genomes]
rs2049301	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs2101398	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2133601	0.84[AMR][1000 genomes]
rs2140335	0.86[AMR][1000 genomes]
rs2631721	0.86[ASN][1000 genomes]
rs2882611	0.86[AMR][1000 genomes]
rs319682	0.84[ASN][1000 genomes]
rs319684	0.83[ASN][1000 genomes]
rs319685	0.83[ASN][1000 genomes]
rs319686	0.83[ASN][1000 genomes]
rs319689	0.83[ASN][1000 genomes]
rs319692	0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs319693	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs319694	0.90[ASN][1000 genomes]
rs319695	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs319696	0.83[ASN][1000 genomes]
rs34025851	0.83[ASN][1000 genomes]
rs34249203	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34351471	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34569417	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34777284	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34906469	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35148469	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35582375	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35698005	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3732529	0.83[ASN][1000 genomes]
rs3755637	0.84[AMR][1000 genomes]
rs3755638	0.81[AMR][1000 genomes]
rs3772399	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3772403	0.81[AMR][1000 genomes]
rs3888	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3915654	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4410463	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs4858846	0.84[AMR][1000 genomes]
rs4858851	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4858853	0.89[EUR][1000 genomes]
rs4858857	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4858860	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4858863	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4858871	0.83[ASN][1000 genomes]
rs55823596	0.88[EUR][1000 genomes]
rs56376646	0.85[EUR][1000 genomes]
rs60110914	0.82[AMR][1000 genomes]
rs60446735	0.83[ASN][1000 genomes]
rs61181421	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62262129	0.83[AMR][1000 genomes]
rs62263561	0.88[EUR][1000 genomes]
rs6442072	0.84[AMR][1000 genomes]
rs6442074	0.84[AMR][1000 genomes]
rs6442079	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6442081	0.85[EUR][1000 genomes]
rs6442082	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6442083	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6442085	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6442086	0.91[EUR][1000 genomes]
rs6768699	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6772301	0.84[AMR][1000 genomes]
rs6772396	0.83[ASN][1000 genomes]
rs6773467	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs6773732	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs6776963	0.93[EUR][1000 genomes]
rs6777632	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6782998	0.82[EUR][1000 genomes]
rs6783629	0.82[ASN][1000 genomes]
rs6785669	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6786001	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6792350	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6792497	0.83[AMR][1000 genomes]
rs6792737	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6806860	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72906488	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73085151	0.88[EUR][1000 genomes]
rs7429162	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7612219	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7613934	0.82[AMR][1000 genomes]
rs7618758	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7621236	0.82[AMR][1000 genomes]
rs7624474	0.82[AMR][1000 genomes]
rs7629850	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7637372	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7637950	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7638103	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7645846	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7646982	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7649393	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs777015	0.83[ASN][1000 genomes]
rs796566	0.81[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs800762	0.84[ASN][1000 genomes]
rs810334	0.83[ASN][1000 genomes]
rs883663	0.83[AMR][1000 genomes]
rs9757517	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9850154	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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	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
rs62263575	MAP4	Cis_1M	lymphoblastoid	RTeQTL
rs62263575	MRPS18AP1	cis	Nerve Tibial	GTEx
rs62263575	MRPS18AP1	cis	Muscle Skeletal	GTEx
rs62263575	MRPS18AP1	cis	lung	GTEx
rs62263575	DHX30	Cis_1M	lymphoblastoid	RTeQTL
rs62263575	ZNF589	cis	Nerve Tibial	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47845600-47859000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:47845600-47866000	Weak transcription	Right Atrium	heart
3	chr3:47845600-47866200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:47845600-47866600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr3:47845800-47866000	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr3:47846200-47856800	Weak transcription	HMEC	breast
7	chr3:47846400-47863800	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr3:47846400-47865800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr3:47846600-47857600	Strong transcription	H1 Cell Line	embryonic stem cell
10	chr3:47846600-47858600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr3:47846600-47859200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
12	chr3:47846600-47863800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr3:47846600-47863800	Strong transcription	Fetal Thymus	thymus
14	chr3:47846600-47864000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr3:47846600-47864000	Strong transcription	Fetal Muscle Leg	muscle
16	chr3:47846600-47864200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr3:47846600-47864200	Strong transcription	Fetal Muscle Trunk	muscle
18	chr3:47846600-47865800	Weak transcription	Fetal Heart	heart
19	chr3:47846800-47857000	Strong transcription	Fetal Intestine Small	intestine
20	chr3:47846800-47863800	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr3:47846800-47864400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr3:47846800-47864600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:47846800-47864800	Strong transcription	Fetal Stomach	stomach
24	chr3:47846800-47865800	Weak transcription	Hela-S3	cervix
25	chr3:47847000-47862400	Strong transcription	Dnd41	blood
26	chr3:47847000-47864000	Strong transcription	Cortex derived primary cultured neurospheres	brain
27	chr3:47847000-47864000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr3:47847400-47860600	Weak transcription	NHDF-Ad	bronchial
29	chr3:47848000-47863400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr3:47848200-47864000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr3:47848600-47861600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr3:47848600-47862400	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr3:47848600-47864000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr3:47848600-47864400	Strong transcription	Thymus	Thymus
35	chr3:47849600-47857600	Strong transcription	Brain Germinal Matrix	brain
36	chr3:47850800-47862400	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr3:47851200-47862600	Strong transcription	Primary B cells from peripheral blood	blood
38	chr3:47851200-47863800	Strong transcription	Stomach Smooth Muscle	stomach
39	chr3:47851600-47857600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr3:47851600-47862200	Strong transcription	Lung	lung
41	chr3:47852000-47856400	Weak transcription	NH-A	brain
42	chr3:47852600-47866200	Weak transcription	Psoas Muscle	Psoas
43	chr3:47853000-47859400	Weak transcription	Pancreas	Pancrea
44	chr3:47853000-47859600	Weak transcription	Colonic Mucosa	Colon
45	chr3:47853000-47860000	Weak transcription	NHLF	lung
46	chr3:47853000-47860400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr3:47853000-47865800	Weak transcription	K562	blood
48	chr3:47853000-47866000	Weak transcription	Small Intestine	intestine
49	chr3:47853200-47856600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr3:47853200-47856600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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