Variant report

Variant	rs4519692
Chromosome Location	chr3:49873188-49873189
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 90 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10049413	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1049256	0.80[ASN][1000 genomes]
rs10865958	0.89[ASN][1000 genomes]
rs10865959	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11130218	0.80[ASN][1000 genomes]
rs11130219	0.80[ASN][1000 genomes]
rs11130221	0.83[ASN][1000 genomes]
rs1128535	0.89[ASN][1000 genomes]
rs11709680	0.80[ASN][1000 genomes]
rs11710675	0.81[ASN][1000 genomes]
rs11714957	0.83[ASN][1000 genomes]
rs11715304	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11716575	0.80[ASN][1000 genomes]
rs11717256	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11717463	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11920900	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12381242	0.80[ASN][1000 genomes]
rs13063621	0.83[ASN][1000 genomes]
rs13084243	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13085679	0.89[ASN][1000 genomes]
rs13086130	0.83[ASN][1000 genomes]
rs13086465	0.81[ASN][1000 genomes]
rs1317140	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13316065	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1491986	0.80[ASN][1000 genomes]
rs1799843	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1799845	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2234385	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2234391	0.87[ASN][1000 genomes]
rs2246832	0.92[ASN][1000 genomes]
rs2247036	0.92[ASN][1000 genomes]
rs2271960	0.92[ASN][1000 genomes]
rs2271961	0.92[ASN][1000 genomes]
rs2276864	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2291542	0.81[ASN][1000 genomes]
rs2307021	0.81[ASN][1000 genomes]
rs2352967	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2352974	0.92[ASN][1000 genomes]
rs2352975	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34451146	0.83[ASN][1000 genomes]
rs34522271	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34614773	0.80[ASN][1000 genomes]
rs34735338	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35210174	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35261599	0.82[ASN][1000 genomes]
rs35474403	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3749237	0.83[ASN][1000 genomes]
rs3749240	0.80[ASN][1000 genomes]
rs3749241	0.80[ASN][1000 genomes]
rs3811696	0.80[ASN][1000 genomes]
rs3819325	0.83[ASN][1000 genomes]
rs4768	0.81[ASN][1000 genomes]
rs4855862	0.80[ASN][1000 genomes]
rs4855867	0.80[ASN][1000 genomes]
rs57648519	0.83[ASN][1000 genomes]
rs59906301	0.81[ASN][1000 genomes]
rs60205400	0.83[ASN][1000 genomes]
rs62260715	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62260719	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62260729	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6446295	0.82[ASN][1000 genomes]
rs6766836	0.83[ASN][1000 genomes]
rs6775384	0.89[ASN][1000 genomes]
rs6802890	0.83[ASN][1000 genomes]
rs695238	0.89[ASN][1000 genomes]
rs71324996	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7431078	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7431106	0.83[ASN][1000 genomes]
rs7618501	0.81[ASN][1000 genomes]
rs7618519	0.82[ASN][1000 genomes]
rs7629936	0.86[ASN][1000 genomes]
rs7634886	0.80[ASN][1000 genomes]
rs7634902	0.80[ASN][1000 genomes]
rs7645061	0.89[ASN][1000 genomes]
rs7648987	0.89[ASN][1000 genomes]
rs7649348	0.82[ASN][1000 genomes]
rs9814765	0.82[ASN][1000 genomes]
rs9815766	0.83[ASN][1000 genomes]
rs9819511	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9850465	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9853458	0.80[ASN][1000 genomes]
rs9859153	0.83[ASN][1000 genomes]
rs9865480	0.80[ASN][1000 genomes]
rs9871654	0.82[ASN][1000 genomes]
rs9876508	0.82[ASN][1000 genomes]
rs9882639	0.83[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	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
2	nsv834688	chr3:49811115-50019299	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	esv1809827	chr3:49812331-49934179	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv876766	chr3:49817450-49961780	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers 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	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4519692	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs4519692	WDR6	cis	Whole Blood	GTEx

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49861200-49882200	Weak transcription	Primary B cells from cord blood	blood
2	chr3:49861200-49893200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr3:49863400-49876800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr3:49863400-49876800	Weak transcription	Brain Substantia Nigra	brain
5	chr3:49863400-49879000	Weak transcription	Fetal Brain Male	brain
6	chr3:49863600-49876600	Weak transcription	Brain Hippocampus Middle	brain
7	chr3:49863800-49874000	Weak transcription	Primary hematopoietic stem cells	blood
8	chr3:49863800-49875600	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr3:49863800-49879000	Weak transcription	NH-A	brain
10	chr3:49863800-49882800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr3:49864000-49876600	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr3:49864000-49883200	Weak transcription	Colonic Mucosa	Colon
13	chr3:49864000-49893200	Weak transcription	Placenta	Placenta
14	chr3:49864200-49876800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr3:49864200-49893000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr3:49864400-49876800	Weak transcription	Brain Anterior Caudate	brain
17	chr3:49864600-49876800	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr3:49864600-49882000	Weak transcription	Osteobl	bone
19	chr3:49864800-49878000	Strong transcription	Fetal Thymus	thymus
20	chr3:49864800-49880400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr3:49864800-49886000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr3:49865000-49876400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:49865000-49876400	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr3:49865000-49886000	Strong transcription	Dnd41	blood
25	chr3:49865200-49876200	Strong transcription	Cortex derived primary cultured neurospheres	brain
26	chr3:49865200-49877000	Weak transcription	Right Ventricle	heart
27	chr3:49865200-49877400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr3:49865600-49876000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr3:49865600-49876800	Weak transcription	Rectal Smooth Muscle	rectum
30	chr3:49865600-49885800	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr3:49865600-49885800	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr3:49866000-49881000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr3:49866200-49876800	Weak transcription	HUVEC	blood vessel
34	chr3:49866600-49876600	Weak transcription	Primary B cells from peripheral blood	blood
35	chr3:49867000-49876800	Weak transcription	Right Atrium	heart
36	chr3:49867200-49876800	Weak transcription	Ovary	ovary
37	chr3:49867600-49876600	Weak transcription	Fetal Lung	lung
38	chr3:49867800-49879000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr3:49868200-49878600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr3:49869000-49876800	Weak transcription	NHLF	lung
41	chr3:49869000-49883200	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr3:49869200-49874600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr3:49869200-49875600	Weak transcription	A549	lung
44	chr3:49869200-49876800	Weak transcription	Brain Germinal Matrix	brain
45	chr3:49869200-49876800	Weak transcription	Esophagus	oesophagus
46	chr3:49869200-49876800	Weak transcription	Hela-S3	cervix
47	chr3:49869200-49879000	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr3:49869200-49881000	Weak transcription	HMEC	breast
49	chr3:49869400-49874200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr3:49869400-49875600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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