Variant report

Variant	rs13077403
Chromosome Location	chr3:49996053-49996054
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs11130222	0.87[ASN][1000 genomes]
rs11706185	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11709503	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11709573	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11712056	0.86[ASN][1000 genomes]
rs11714324	0.91[ASN][1000 genomes]
rs11721204	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12107768	0.82[ASN][1000 genomes]
rs12634780	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13079006	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13082703	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17657664	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17657688	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2352969	0.98[ASN][1000 genomes]
rs2352984	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2526747	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2526749	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2526750	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2624815	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2624819	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2624821	0.95[ASN][1000 genomes]
rs2624822	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2624832	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2681776	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2681779	0.85[ASN][1000 genomes]
rs2883059	0.87[ASN][1000 genomes]
rs34034116	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34312088	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34654589	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs35275715	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36022378	0.84[ASN][1000 genomes]
rs3733134	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3774734	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3774759	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3796386	0.87[ASN][1000 genomes]
rs4688688	0.91[ASN][1000 genomes]
rs4688753	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4688754	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55692411	0.88[ASN][1000 genomes]
rs62262114	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6446191	0.89[EUR][1000 genomes]
rs6446192	0.85[EUR][1000 genomes]
rs6446194	0.84[EUR][1000 genomes]
rs6446195	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6446197	0.81[EUR][1000 genomes]
rs6762477	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6774354	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6793528	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6799579	0.82[ASN][1000 genomes]
rs7061	0.80[ASN][1000 genomes]
rs7430334	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7613360	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7615206	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7626952	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7627864	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7627910	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7634441	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7648174	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs868891	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs952594	0.89[ASN][1000 genomes]
rs9682295	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9812936	0.84[EUR][1000 genomes]
rs9844201	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv876767	chr3:49918751-50153356	Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv834689	chr3:49962930-50085119	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv965334	chr3:49967342-50000012	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
5	nsv1012903	chr3:49978765-50071878	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs13077403	RBM6	cis	Thyroid	GTEx
rs13077403	RBM6	cis	Skin Sun Exposed Lower leg	GTEx
rs13077403	RBM6	cis	Artery Aorta	GTEx
rs13077403	RBM6	cis	Artery Tibial	GTEx
rs13077403	RBM6	cis	Esophagus Muscularis	GTEx
rs13077403	RBM6	cis	Nerve Tibial	GTEx
rs13077403	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs13077403	RBM6	cis	Adipose Subcutaneous	GTEx
rs13077403	RBM6	cis	Esophagus Mucosa	GTEx
rs13077403	RBM6	cis	Heart Left Ventricle	GTEx
rs13077403	RBM6	cis	Whole Blood	GTEx
rs13077403	RBM6	cis	lung	GTEx

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49978800-50000600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr3:49978800-50004800	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr3:49978800-50009600	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr3:49978800-50009600	Weak transcription	Fetal Kidney	kidney
5	chr3:49978800-50041000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr3:49979000-49997400	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr3:49979000-50000000	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr3:49979000-50000600	Weak transcription	Primary T cells from cord blood	blood
9	chr3:49979000-50001000	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr3:49979000-50003400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr3:49979000-50003600	Weak transcription	Right Ventricle	heart
12	chr3:49979000-50005200	Weak transcription	Fetal Muscle Trunk	muscle
13	chr3:49979000-50010200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr3:49979400-49999000	Weak transcription	Fetal Thymus	thymus
15	chr3:49979400-49999600	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr3:49979400-50000400	Weak transcription	Brain Germinal Matrix	brain
17	chr3:49979600-49999800	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr3:49979600-50004200	Weak transcription	Primary hematopoietic stem cells	blood
19	chr3:49980400-49997400	Weak transcription	HepG2	liver
20	chr3:49980400-50003600	Weak transcription	Brain Angular Gyrus	brain
21	chr3:49980600-49999600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr3:49980600-50000000	Weak transcription	Dnd41	blood
23	chr3:49980600-50001800	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr3:49981400-49999800	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr3:49981600-49999600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr3:49983800-49997600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:49983800-49999200	Weak transcription	Fetal Muscle Leg	muscle
28	chr3:49983800-50003400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr3:49984000-49998200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr3:49984000-50000400	Weak transcription	Fetal Intestine Large	intestine
31	chr3:49984200-49998400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr3:49985600-50000600	Weak transcription	Primary B cells from cord blood	blood
33	chr3:49986000-50000600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr3:49987000-49997400	Weak transcription	Right Atrium	heart
35	chr3:49987600-49997800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr3:49987800-49997400	Weak transcription	Primary B cells from peripheral blood	blood
37	chr3:49988000-49997200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr3:49988000-49997400	Weak transcription	Left Ventricle	heart
39	chr3:49988000-50000600	Weak transcription	Duodenum Mucosa	Duodenum
40	chr3:49988000-50003000	Weak transcription	NHEK	skin
41	chr3:49988000-50003600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr3:49988000-50004200	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr3:49988200-49997200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr3:49988200-49997400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr3:49988200-49997400	Weak transcription	Ovary	ovary
46	chr3:49988200-50007000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr3:49988200-50007400	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr3:49988200-50010200	Weak transcription	Gastric	stomach
49	chr3:49988200-50010600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr3:49988400-49996200	Weak transcription	HMEC	breast

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