Variant report

Variant	rs2101398
Chromosome Location	chr3:47850169-47850170
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:47843708..47846304-chr3:47849542..47851138,2	K562	blood:
2	chr3:47842974..47845357-chr3:47848798..47852867,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000132153	Chromatin interaction

Extended variants
information (count: 132 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:130)

rs_ID	r²[population]
rs1061003	0.86[AFR][1000 genomes]
rs10865948	0.80[AMR][1000 genomes]
rs11130145	0.87[AMR][1000 genomes]
rs11130146	0.88[AMR][1000 genomes]
rs11130147	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11130148	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11130150	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11708849	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11710199	0.86[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs11712464	0.85[EUR][1000 genomes]
rs11714942	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11716582	0.81[AMR][1000 genomes]
rs11927129	0.85[EUR][1000 genomes]
rs12492915	0.83[AMR][1000 genomes]
rs12495204	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12497921	0.83[AMR][1000 genomes]
rs12498027	0.85[AMR][1000 genomes]
rs12633604	0.86[AMR][1000 genomes]
rs13061412	0.84[AMR][1000 genomes]
rs13063042	0.85[AMR][1000 genomes]
rs13064183	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13070035	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13077230	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13079407	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13081356	0.87[AMR][1000 genomes]
rs13086149	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13091913	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13094264	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13098128	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1403578	0.81[AMR][1000 genomes]
rs1403579	0.81[AMR][1000 genomes]
rs1486915	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1684942	0.85[AFR][1000 genomes]
rs17079785	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17290490	0.86[AFR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2030596	0.83[AMR][1000 genomes]
rs2047559	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2049301	0.82[AMR][1000 genomes]
rs2133601	0.85[AMR][1000 genomes]
rs2140335	0.88[AMR][1000 genomes]
rs2293226	0.81[AMR][1000 genomes]
rs2631721	0.83[AFR][1000 genomes]
rs2882611	0.81[AMR][1000 genomes]
rs2882668	0.81[AFR][1000 genomes]
rs319680	0.84[AFR][1000 genomes]
rs319682	0.83[AFR][1000 genomes]
rs319684	0.83[AFR][1000 genomes]
rs319685	0.81[AFR][1000 genomes]
rs319687	0.84[AFR][1000 genomes]
rs319689	0.84[AFR][1000 genomes]
rs319690	0.83[AFR][1000 genomes]
rs319691	0.81[AFR][1000 genomes]
rs319693	0.86[EUR][1000 genomes]
rs319694	0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs34249203	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34351471	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34569417	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34777284	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34906469	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35148469	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35582375	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35698005	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3755638	0.80[AMR][1000 genomes]
rs3772399	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3772403	0.80[AMR][1000 genomes]
rs3888	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3915654	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4410463	0.82[AMR][1000 genomes]
rs4858801	0.81[AMR][1000 genomes]
rs4858803	0.83[AMR][1000 genomes]
rs4858842	0.81[AMR][1000 genomes]
rs4858846	0.85[AMR][1000 genomes]
rs4858851	0.82[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]
rs4858860	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4858863	0.95[EUR][1000 genomes]
rs55823596	0.88[EUR][1000 genomes]
rs56376646	0.85[EUR][1000 genomes]
rs61181421	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61620099	0.81[AMR][1000 genomes]
rs62262129	0.84[AMR][1000 genomes]
rs62263561	0.88[EUR][1000 genomes]
rs62263575	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6442074	0.85[AMR][1000 genomes]
rs6442079	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6442081	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6442082	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6442083	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6442085	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6442086	0.91[EUR][1000 genomes]
rs6768699	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6772301	0.85[AMR][1000 genomes]
rs6773467	0.82[AMR][1000 genomes]
rs6773732	0.82[AMR][1000 genomes]
rs6774170	0.80[AMR][1000 genomes]
rs6776963	0.93[EUR][1000 genomes]
rs6777632	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6782998	0.82[AMR][1000 genomes]
rs6785669	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6786001	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6792350	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6792497	0.84[AMR][1000 genomes]
rs6792737	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6806860	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72906488	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73085151	0.88[EUR][1000 genomes]
rs7429162	0.82[AMR][1000 genomes]
rs7612219	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7613934	0.83[AMR][1000 genomes]
rs7618758	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7621236	0.83[AMR][1000 genomes]
rs7624474	0.83[AMR][1000 genomes]
rs7629850	0.95[EUR][1000 genomes]
rs7631950	0.81[AMR][1000 genomes]
rs7637372	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7637950	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7638103	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7645846	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7646982	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7649393	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7653368	0.81[AFR][1000 genomes]
rs777015	0.81[AFR][1000 genomes]
rs800762	0.85[AFR][1000 genomes]
rs810334	0.81[AFR][1000 genomes]
rs868255	0.81[AMR][1000 genomes]
rs870622	0.81[AMR][1000 genomes]
rs883661	0.81[AMR][1000 genomes]
rs9757517	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9850154	0.86[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2101398	MRPS18AP1	cis	Nerve Tibial	GTEx
rs2101398	MAP4	Cis_1M	lymphoblastoid	RTeQTL
rs2101398	MRPS18AP1	cis	Muscle Skeletal	GTEx
rs2101398	ZNF589	cis	Nerve Tibial	GTEx
rs2101398	DHX30	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47845400-47852000	Weak transcription	Aorta	Aorta
2	chr3:47845600-47850800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr3:47845600-47851000	Weak transcription	Esophagus	oesophagus
4	chr3:47845600-47851600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:47845600-47851600	Weak transcription	Colonic Mucosa	Colon
6	chr3:47845600-47852000	Weak transcription	Gastric	stomach
7	chr3:47845600-47852000	Weak transcription	Pancreas	Pancrea
8	chr3:47845600-47859000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr3:47845600-47866000	Weak transcription	Right Atrium	heart
10	chr3:47845600-47866200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr3:47845600-47866600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr3:47845800-47850400	Weak transcription	Osteobl	bone
13	chr3:47845800-47850600	Weak transcription	Adipose Nuclei	Adipose
14	chr3:47845800-47851000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr3:47845800-47851000	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr3:47845800-47851200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr3:47845800-47851200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr3:47845800-47851200	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr3:47845800-47851200	Weak transcription	HSMM	muscle
20	chr3:47845800-47851600	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr3:47845800-47851800	Weak transcription	Stomach Mucosa	stomach
22	chr3:47845800-47851800	Weak transcription	NHLF	lung
23	chr3:47845800-47852000	Weak transcription	Psoas Muscle	Psoas
24	chr3:47845800-47866000	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr3:47846000-47851400	Weak transcription	Primary hematopoietic stem cells	blood
26	chr3:47846000-47851400	Weak transcription	Fetal Brain Male	brain
27	chr3:47846000-47852000	Weak transcription	Right Ventricle	heart
28	chr3:47846200-47851200	Weak transcription	HSMMtube	muscle
29	chr3:47846200-47851200	Weak transcription	NH-A	brain
30	chr3:47846200-47851600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr3:47846200-47851600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr3:47846200-47851600	Weak transcription	Rectal Smooth Muscle	rectum
33	chr3:47846200-47851600	Weak transcription	K562	blood
34	chr3:47846200-47851800	Weak transcription	Primary B cells from cord blood	blood
35	chr3:47846200-47852600	Weak transcription	Small Intestine	intestine
36	chr3:47846200-47856800	Weak transcription	HMEC	breast
37	chr3:47846400-47851000	Weak transcription	HepG2	liver
38	chr3:47846400-47851200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr3:47846400-47851600	Weak transcription	Colon Smooth Muscle	Colon
40	chr3:47846400-47851600	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr3:47846400-47852000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr3:47846400-47854800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr3:47846400-47863800	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr3:47846400-47865800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr3:47846600-47851000	Weak transcription	GM12878-XiMat	blood
46	chr3:47846600-47851200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr3:47846600-47851200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr3:47846600-47851200	Weak transcription	A549	lung
49	chr3:47846600-47852000	Weak transcription	NHEK	skin
50	chr3:47846600-47855600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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