Variant report

Variant	rs9848497
Chromosome Location	chr3:49951316-49951317
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:49949742..49951571-chr3:49951918..49953563,2	K562	blood:
2	chr3:49870527..49872385-chr3:49950904..49952666,2	MCF-7	breast:
3	chr3:49938059..49942397-chr3:49945875..49951610,6	K562	blood:

Variant related genes	Relation type
ENSG00000164078	Chromatin interaction
ENSG00000228008	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1062633	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11130224	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11130226	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11130228	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130229	0.87[ASN][1000 genomes]
rs11130233	0.90[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11130234	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11713193	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11713562	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11925192	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12485600	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12496973	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13060128	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1317154	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2230590	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2252833	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2280406	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2353579	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2353586	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2353587	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2526751	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2624843	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2624844	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2681778	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2681780	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2681781	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2777888	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2883057	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34080578	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35065728	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3733135	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3774733	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3774758	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4688689	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4688690	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4688755	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4688756	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4688757	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4688758	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55751738	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62262093	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6446187	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6446189	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6446193	0.82[ASN][1000 genomes]
rs6765484	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6767381	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6771546	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6772095	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6780731	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6792892	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6795703	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72942333	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7609971	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7613875	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7621026	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7621352	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7628058	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7634084	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7635002	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9821433	0.83[ASN][1000 genomes]
rs9821675	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9843653	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9853222	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9861216	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9862795	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9866695	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	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
3	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

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs9848497	RBM6	cis	Esophagus Mucosa	GTEx
rs9848497	RBM6	cis	Heart Left Ventricle	GTEx
rs9848497	RBM6	cis	Esophagus Muscularis	GTEx
rs9848497	RBM6	cis	Adipose Subcutaneous	GTEx
rs9848497	RBM6	cis	Nerve Tibial	GTEx
rs9848497	RBM6	cis	Stomach	GTEx
rs9848497	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs9848497	ACTBP13	cis	Skin Sun Exposed Lower leg	GTEx
rs9848497	RBM6	cis	Thyroid	GTEx
rs9848497	FAM212A	cis	Esophagus Mucosa	GTEx
rs9848497	RBM6	cis	Artery Aorta	GTEx
rs9848497	RBM6	cis	lung	GTEx
rs9848497	RBM6	cis	Whole Blood	GTEx
rs9848497	RBM6	cis	Artery Tibial	GTEx
rs9848497	RBM6	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49943800-49966000	Weak transcription	Psoas Muscle	Psoas
2	chr3:49944000-49954000	Weak transcription	NHDF-Ad	bronchial
3	chr3:49944200-49956200	Weak transcription	Primary hematopoietic stem cells	blood
4	chr3:49944200-49962000	Weak transcription	HepG2	liver
5	chr3:49944200-49962000	Weak transcription	HSMM	muscle
6	chr3:49944200-49962000	Weak transcription	NH-A	brain
7	chr3:49944200-49966000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr3:49944400-49952600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr3:49944400-49952800	Weak transcription	GM12878-XiMat	blood
10	chr3:49944400-49955000	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr3:49944400-49966000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr3:49944400-49966000	Weak transcription	HUVEC	blood vessel
13	chr3:49944600-49961800	Weak transcription	Hela-S3	cervix
14	chr3:49944800-49951400	Strong transcription	Fetal Muscle Leg	muscle
15	chr3:49945600-49951400	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr3:49946000-49951400	Strong transcription	Lung	lung
17	chr3:49946200-49951400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr3:49946400-49951400	Strong transcription	Duodenum Mucosa	Duodenum
19	chr3:49946600-49952000	Strong transcription	Fetal Intestine Small	intestine
20	chr3:49946800-49965800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr3:49948000-49952600	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr3:49948000-49961600	Weak transcription	HMEC	breast
23	chr3:49948000-49966800	Weak transcription	Fetal Heart	heart
24	chr3:49948200-49953800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr3:49948400-49952800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr3:49948400-49954200	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr3:49948600-49965400	Weak transcription	Fetal Lung	lung
28	chr3:49948800-49952400	Weak transcription	K562	blood
29	chr3:49948800-49961800	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr3:49948800-49966000	Weak transcription	Primary B cells from peripheral blood	blood
31	chr3:49949000-49966200	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr3:49949200-49954400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr3:49949400-49962200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr3:49949400-49965600	Weak transcription	Brain Hippocampus Middle	brain
35	chr3:49949600-49954200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr3:49949800-49951600	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr3:49949800-49953200	Weak transcription	Esophagus	oesophagus
38	chr3:49949800-49965400	Weak transcription	Gastric	stomach
39	chr3:49949800-49965800	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr3:49949800-49966800	Weak transcription	Aorta	Aorta
41	chr3:49950000-49954400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr3:49950000-49965800	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr3:49950200-49962200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr3:49950200-49966000	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr3:49950400-49954000	Weak transcription	Osteobl	bone
46	chr3:49950400-49965400	Weak transcription	Right Ventricle	heart
47	chr3:49950400-49965800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr3:49950600-49952200	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr3:49950600-49954000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr3:49950600-49956800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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