Variant report

Variant	rs3749241
Chromosome Location	chr3:49744392-49744393
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:49741441..49744907-chr3:49939515..49942353,3	K562	blood:
2	chr3:49741563..49745269-chr3:49756251..49759503,3	K562	blood:
3	chr3:49743020..49745371-chr3:49755565..49758428,3	K562	blood:
4	chr3:49742940..49745139-chr3:49760029..49761535,2	K562	blood:

Variant related genes	Relation type
ENSG00000173540	Chromatin interaction
ENSG00000176020	Chromatin interaction
ENSG00000164068	Chromatin interaction
ENSG00000228008	Chromatin interaction
ENSG00000164078	Chromatin interaction

Extended variants
information (count: 110 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10049413	0.84[ASN][1000 genomes]
rs1049256	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10865958	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10865959	0.84[ASN][1000 genomes]
rs11130214	0.96[ASN][1000 genomes]
rs11130216	0.96[ASN][1000 genomes]
rs11130218	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11130219	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11130221	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1128535	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11709680	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11710675	0.99[ASN][1000 genomes]
rs11714957	0.96[ASN][1000 genomes]
rs11715304	0.88[ASN][1000 genomes]
rs11716575	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11717256	0.87[ASN][1000 genomes]
rs11717463	0.96[ASN][1000 genomes]
rs11920900	0.95[ASN][1000 genomes]
rs12381242	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12490656	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12496226	0.92[ASN][1000 genomes]
rs13063621	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13084243	0.96[ASN][1000 genomes]
rs13085679	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13086130	0.96[ASN][1000 genomes]
rs13086465	0.94[ASN][1000 genomes]
rs13090611	0.88[ASN][1000 genomes]
rs1317140	0.80[ASN][1000 genomes]
rs13316065	0.85[ASN][1000 genomes]
rs1491986	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1799843	0.89[ASN][1000 genomes]
rs1799845	0.89[ASN][1000 genomes]
rs2234385	0.89[ASN][1000 genomes]
rs2234391	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2246832	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2247036	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2271960	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2271961	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2276864	0.84[ASN][1000 genomes]
rs2291542	0.99[ASN][1000 genomes]
rs2307021	0.99[ASN][1000 genomes]
rs2352967	0.85[ASN][1000 genomes]
rs2352974	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2352975	0.84[ASN][1000 genomes]
rs34451146	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34522271	0.96[ASN][1000 genomes]
rs34614773	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34735338	0.94[ASN][1000 genomes]
rs35210174	0.96[ASN][1000 genomes]
rs35261599	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35474403	0.96[ASN][1000 genomes]
rs3749237	0.96[ASN][1000 genomes]
rs3749240	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3811695	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3811696	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3819325	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4519692	0.80[ASN][1000 genomes]
rs4768	0.99[ASN][1000 genomes]
rs4855841	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4855850	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4855862	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4855867	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57648519	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59906301	0.92[ASN][1000 genomes]
rs60205400	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62260715	0.94[ASN][1000 genomes]
rs62260719	0.89[ASN][1000 genomes]
rs62260729	0.84[ASN][1000 genomes]
rs6446295	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6766836	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6775384	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6785549	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6802890	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6804655	0.96[ASN][1000 genomes]
rs695238	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs71324996	0.80[ASN][1000 genomes]
rs7372725	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7372730	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7372966	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7374183	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7374277	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7426497	0.87[AMR][1000 genomes]
rs7429353	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7431078	0.96[ASN][1000 genomes]
rs7431106	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7618501	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7618519	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7629936	0.88[ASN][1000 genomes]
rs7634886	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7634902	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7645061	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7648987	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7649348	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9814765	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9815766	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9819511	0.84[ASN][1000 genomes]
rs9850465	0.86[ASN][1000 genomes]
rs9853458	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9855505	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9859153	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9865480	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9871654	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9872864	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9873183	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9876508	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9882639	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][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	nsv508217	chr3:49615446-49769896	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	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
3	esv1825898	chr3:49688948-49764849	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
4	esv1808511	chr3:49689880-49744825	Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs3749241	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs3749241	RBM6	cis	Nerve Tibial	GTEx
rs3749241	RBM6	cis	Artery Tibial	GTEx
rs3749241	UBA7	cis	Whole Blood	GTEx
rs3749241	RBM6	cis	Esophagus Muscularis	GTEx
rs3749241	RBM6	cis	Adipose Subcutaneous	GTEx
rs3749241	RBM6	cis	Thyroid	GTEx
rs3749241	FAM212A	cis	Esophagus Mucosa	GTEx
rs3749241	RBM6	cis	Whole Blood	GTEx
rs3749241	RBM6	cis	lung	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49728000-49744400	Weak transcription	NH-A	brain
2	chr3:49728000-49748800	Weak transcription	A549	lung
3	chr3:49728400-49753200	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr3:49728400-49756600	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr3:49728600-49744800	Weak transcription	HMEC	breast
6	chr3:49728600-49750400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr3:49729200-49749800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr3:49729200-49750200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr3:49729200-49755800	Weak transcription	Right Atrium	heart
10	chr3:49729400-49750200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr3:49732200-49755000	Strong transcription	Fetal Intestine Small	intestine
12	chr3:49733000-49750200	Weak transcription	Psoas Muscle	Psoas
13	chr3:49734200-49746000	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr3:49734200-49746000	Strong transcription	Thymus	Thymus
15	chr3:49734200-49746200	Strong transcription	Duodenum Mucosa	Duodenum
16	chr3:49734400-49744400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr3:49734400-49744800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr3:49734400-49744800	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr3:49734400-49745000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr3:49734400-49745200	Strong transcription	Fetal Brain Female	brain
21	chr3:49734400-49745400	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr3:49734400-49745400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr3:49734400-49746000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr3:49734400-49746000	Strong transcription	Fetal Intestine Large	intestine
25	chr3:49734400-49746200	Strong transcription	Brain Inferior Temporal Lobe	brain
26	chr3:49734400-49746200	Strong transcription	Stomach Smooth Muscle	stomach
27	chr3:49734400-49746200	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr3:49734400-49746400	Strong transcription	Brain Hippocampus Middle	brain
29	chr3:49734400-49756000	Strong transcription	Liver	Liver
30	chr3:49734600-49744800	Strong transcription	Brain Cingulate Gyrus	brain
31	chr3:49734600-49744800	Strong transcription	Sigmoid Colon	Sigmoid Colon
32	chr3:49734600-49745000	Strong transcription	Esophagus	oesophagus
33	chr3:49734600-49745000	Strong transcription	Dnd41	blood
34	chr3:49734600-49745400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr3:49734600-49745400	Strong transcription	Brain Germinal Matrix	brain
36	chr3:49734600-49746000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr3:49734600-49746200	Strong transcription	Fetal Muscle Leg	muscle
38	chr3:49734600-49746400	Strong transcription	Fetal Thymus	thymus
39	chr3:49734800-49745400	Strong transcription	Cortex derived primary cultured neurospheres	brain
40	chr3:49734800-49746200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr3:49734800-49746200	Strong transcription	Brain Anterior Caudate	brain
42	chr3:49735400-49755400	Weak transcription	Stomach Mucosa	stomach
43	chr3:49736000-49749800	Weak transcription	GM12878-XiMat	blood
44	chr3:49736000-49753000	Weak transcription	K562	blood
45	chr3:49736600-49746000	Strong transcription	Right Ventricle	heart
46	chr3:49736800-49745200	Strong transcription	Placenta Amnion	Placenta Amnion
47	chr3:49736800-49756400	Weak transcription	HSMM	muscle
48	chr3:49737000-49744400	Weak transcription	NHDF-Ad	bronchial
49	chr3:49737200-49746000	Strong transcription	Ovary	ovary
50	chr3:49737200-49746200	Strong transcription	Adipose Nuclei	Adipose

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