Variant report

Variant	rs9853458
Chromosome Location	chr3:49783211-49783212
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49780730..49783589-chr3:49785334..49787820,2	K562	blood:
2	chr3:49782178..49785035-chr3:49823443..49825758,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000176095	Chromatin interaction

Extended variants
information (count: 106 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10049413	0.86[ASN][1000 genomes]
rs1049256	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10865958	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10865959	0.86[ASN][1000 genomes]
rs11130214	0.94[ASN][1000 genomes]
rs11130216	0.94[ASN][1000 genomes]
rs11130218	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11130219	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11130221	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1128535	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11709680	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11710675	0.92[ASN][1000 genomes]
rs11714957	0.94[ASN][1000 genomes]
rs11715304	0.88[ASN][1000 genomes]
rs11716575	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11717256	0.89[ASN][1000 genomes]
rs11717463	0.94[ASN][1000 genomes]
rs11920900	0.93[ASN][1000 genomes]
rs12381242	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12490656	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12496226	0.89[ASN][1000 genomes]
rs13063621	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13084243	0.94[ASN][1000 genomes]
rs13085679	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13086130	0.94[ASN][1000 genomes]
rs13086465	0.92[ASN][1000 genomes]
rs13090611	0.90[ASN][1000 genomes]
rs1317140	0.80[ASN][1000 genomes]
rs13316065	0.85[ASN][1000 genomes]
rs1491986	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1799843	0.87[ASN][1000 genomes]
rs1799845	0.87[ASN][1000 genomes]
rs2234385	0.87[ASN][1000 genomes]
rs2234391	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2246832	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2247036	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2271960	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2271961	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2276864	0.86[ASN][1000 genomes]
rs2291542	0.92[ASN][1000 genomes]
rs2307021	0.92[ASN][1000 genomes]
rs2352967	0.85[ASN][1000 genomes]
rs2352974	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2352975	0.86[ASN][1000 genomes]
rs34451146	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34522271	0.94[ASN][1000 genomes]
rs34614773	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34735338	0.92[ASN][1000 genomes]
rs35210174	0.94[ASN][1000 genomes]
rs35261599	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35474403	0.94[ASN][1000 genomes]
rs3749237	0.94[ASN][1000 genomes]
rs3749240	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3749241	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3811695	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3811696	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3819325	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4519692	0.80[ASN][1000 genomes]
rs4768	0.92[ASN][1000 genomes]
rs4855841	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4855850	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4855862	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4855867	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57648519	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59906301	0.89[ASN][1000 genomes]
rs60205400	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62260715	0.92[ASN][1000 genomes]
rs62260719	0.87[ASN][1000 genomes]
rs62260729	0.86[ASN][1000 genomes]
rs6446295	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6766836	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6775384	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6785549	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6802890	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6804655	0.94[ASN][1000 genomes]
rs695238	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7372725	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7372730	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7372966	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7374183	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7374277	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7426497	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7429353	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7431078	0.94[ASN][1000 genomes]
rs7431106	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7618501	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7618519	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7629936	0.86[ASN][1000 genomes]
rs7634886	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7634902	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7645061	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7648987	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7649348	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9814765	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9815766	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9819511	0.84[ASN][1000 genomes]
rs9850465	0.83[ASN][1000 genomes]
rs9855505	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9859153	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9865480	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9871654	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9872864	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9873183	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9876508	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9882639	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1796352	chr3:49687101-49949959	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs9853458	RBM6	cis	Esophagus Muscularis	GTEx
rs9853458	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs9853458	RBM6	cis	Artery Tibial	GTEx
rs9853458	RBM6	cis	Nerve Tibial	GTEx
rs9853458	RBM6	cis	Whole Blood	GTEx
rs9853458	RBM6	cis	Adipose Subcutaneous	GTEx
rs9853458	RBM6	cis	Thyroid	GTEx
rs9853458	UBA7	cis	Whole Blood	GTEx
rs9853458	FAM212A	cis	Esophagus Mucosa	GTEx
rs9853458	RBM6	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49762600-49785200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr3:49762600-49809000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr3:49763000-49784800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr3:49765800-49785800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr3:49767600-49787800	Strong transcription	Duodenum Mucosa	Duodenum
6	chr3:49768200-49787600	Strong transcription	Primary B cells from peripheral blood	blood
7	chr3:49772600-49785400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr3:49772600-49791600	Weak transcription	Right Atrium	heart
9	chr3:49774000-49788200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr3:49775600-49783400	Weak transcription	NH-A	brain
11	chr3:49775600-49788200	Weak transcription	Stomach Mucosa	stomach
12	chr3:49775600-49817000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr3:49775800-49810200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr3:49775800-49823000	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr3:49776000-49783400	Weak transcription	Rectal Smooth Muscle	rectum
16	chr3:49776000-49783400	Weak transcription	Right Ventricle	heart
17	chr3:49776000-49783400	Weak transcription	HUVEC	blood vessel
18	chr3:49776000-49784000	Weak transcription	A549	lung
19	chr3:49776000-49784600	Weak transcription	Left Ventricle	heart
20	chr3:49776000-49785200	Weak transcription	GM12878-XiMat	blood
21	chr3:49776000-49789400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr3:49776000-49791200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr3:49776000-49791800	Weak transcription	Psoas Muscle	Psoas
24	chr3:49776200-49783400	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr3:49776200-49784200	Weak transcription	Brain Hippocampus Middle	brain
26	chr3:49776200-49784800	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr3:49776200-49784800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr3:49776200-49784800	Weak transcription	Aorta	Aorta
29	chr3:49776200-49784800	Weak transcription	Liver	Liver
30	chr3:49776200-49784800	Weak transcription	Brain Germinal Matrix	brain
31	chr3:49776200-49784800	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr3:49776200-49785200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr3:49776200-49785200	Weak transcription	Colonic Mucosa	Colon
34	chr3:49776200-49790400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr3:49776200-49799000	Weak transcription	Fetal Heart	heart
36	chr3:49776200-49802000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr3:49776400-49783400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr3:49776400-49783400	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr3:49776400-49783400	Weak transcription	Ovary	ovary
40	chr3:49776400-49783600	Weak transcription	Colon Smooth Muscle	Colon
41	chr3:49776400-49784000	Weak transcription	HepG2	liver
42	chr3:49776400-49784200	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr3:49776400-49784200	Weak transcription	Fetal Brain Female	brain
44	chr3:49776400-49784800	Weak transcription	Brain Substantia Nigra	brain
45	chr3:49776400-49784800	Weak transcription	HMEC	breast
46	chr3:49776400-49785000	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr3:49776400-49785000	Weak transcription	Stomach Smooth Muscle	stomach
48	chr3:49776400-49785200	Weak transcription	Esophagus	oesophagus
49	chr3:49776400-49785200	Weak transcription	Pancreas	Pancrea
50	chr3:49776400-49785200	Weak transcription	Spleen	Spleen

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