Variant report

Variant	rs6446187
Chromosome Location	chr3:49907111-49907112
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	chr3:49897011..49898757-chr3:49905892..49907446,2	K562	blood:
2	chr3:49896228..49898642-chr3:49905668..49907907,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164076	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 14 )

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

rs_ID	r²[population]
rs1062633	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11130224	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11130226	0.94[ASN][1000 genomes]
rs11130228	0.93[ASN][1000 genomes]
rs11130229	0.84[ASN][1000 genomes]
rs11130233	0.92[ASN][1000 genomes]
rs11130234	0.92[ASN][1000 genomes]
rs11713193	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11713562	0.81[ASN][1000 genomes]
rs11925192	0.92[ASN][1000 genomes]
rs12485600	0.92[ASN][1000 genomes]
rs12496973	0.93[ASN][1000 genomes]
rs13060128	0.92[ASN][1000 genomes]
rs1317154	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2230590	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2252833	0.93[ASN][1000 genomes]
rs2280406	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2353579	0.92[ASN][1000 genomes]
rs2353586	0.83[ASN][1000 genomes]
rs2353587	0.82[ASN][1000 genomes]
rs2526751	0.81[ASN][1000 genomes]
rs2624843	0.93[ASN][1000 genomes]
rs2624844	0.84[ASN][1000 genomes]
rs2681778	0.88[ASN][1000 genomes]
rs2681780	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2681781	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2777888	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2883057	0.93[ASN][1000 genomes]
rs34080578	0.92[ASN][1000 genomes]
rs35065728	0.90[ASN][1000 genomes]
rs3733135	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3774733	0.92[ASN][1000 genomes]
rs3774758	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4688689	0.92[ASN][1000 genomes]
rs4688690	0.92[ASN][1000 genomes]
rs4688755	0.81[ASN][1000 genomes]
rs4688756	0.92[ASN][1000 genomes]
rs4688757	0.92[ASN][1000 genomes]
rs4688758	0.92[ASN][1000 genomes]
rs55751738	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs62262093	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6446189	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6446193	0.81[ASN][1000 genomes]
rs6765484	0.92[ASN][1000 genomes]
rs6767381	0.92[ASN][1000 genomes]
rs6771546	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6772095	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6780731	0.92[ASN][1000 genomes]
rs6792892	0.94[ASN][1000 genomes]
rs6795703	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72942333	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7609971	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7613875	0.94[ASN][1000 genomes]
rs7621026	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7621352	0.81[ASN][1000 genomes]
rs7628058	0.92[ASN][1000 genomes]
rs7634084	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7635002	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9821433	0.88[ASN][1000 genomes]
rs9821675	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9843653	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9848497	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9853222	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9861216	0.81[ASN][1000 genomes]
rs9862795	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9866695	0.81[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:14)

SNP	Gene	Cis/trans	Tissue	Source
rs6446187	RBM6	cis	Artery Aorta	GTEx
rs6446187	RBM6	cis	lung	GTEx
rs6446187	FAM212A	cis	Esophagus Mucosa	GTEx
rs6446187	RBM6	cis	Artery Tibial	GTEx
rs6446187	RBM6	cis	Heart Left Ventricle	GTEx
rs6446187	RBM6	cis	Whole Blood	GTEx
rs6446187	RBM6	cis	Esophagus Muscularis	GTEx
rs6446187	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs6446187	RBM6	cis	Nerve Tibial	GTEx
rs6446187	RBM6	cis	Adipose Subcutaneous	GTEx
rs6446187	RBM6	cis	Skin Sun Exposed Lower leg	GTEx
rs6446187	RBM6	cis	Esophagus Mucosa	GTEx
rs6446187	RBM6	cis	Stomach	GTEx
rs6446187	RBM6	cis	Thyroid	GTEx

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49905400-49907600	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
2	chr3:49905800-49907600	Active TSS	Fetal Brain Female	brain
3	chr3:49906200-49907200	Bivalent Enhancer	Fetal Lung	lung
4	chr3:49906200-49907600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
5	chr3:49906200-49907600	Active TSS	Brain Angular Gyrus	brain
6	chr3:49906200-49907600	Enhancers	Gastric	stomach
7	chr3:49906200-49907600	Enhancers	Pancreas	Pancrea
8	chr3:49906200-49907800	Active TSS	H9 Cell Line	embryonic stem cell
9	chr3:49906200-49908200	Active TSS	Brain Anterior Caudate	brain
10	chr3:49906400-49907200	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr3:49906400-49907200	Enhancers	Liver	Liver
12	chr3:49906400-49907200	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
13	chr3:49906400-49907200	Bivalent Enhancer	Small Intestine	intestine
14	chr3:49906400-49907400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
15	chr3:49906400-49907400	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
16	chr3:49906400-49907400	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
17	chr3:49906400-49907600	Active TSS	HUES48 Cell Line	embryonic stem cell
18	chr3:49906400-49907600	Active TSS	iPS-15b Cell Line	embryonic stem cell
19	chr3:49906400-49907600	Active TSS	iPS-18 Cell Line	embryonic stem cell
20	chr3:49906400-49907600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr3:49906400-49907800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr3:49906400-49907800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
23	chr3:49906400-49907800	Bivalent Enhancer	Stomach Mucosa	stomach
24	chr3:49906600-49907200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
25	chr3:49906600-49907200	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
26	chr3:49906600-49907200	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
27	chr3:49906600-49907200	Enhancers	Fetal Heart	heart
28	chr3:49906600-49907400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:49906600-49907400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr3:49906600-49907400	Active TSS	HUES6 Cell Line	embryonic stem cell
31	chr3:49906600-49907400	Bivalent/Poised TSS	Fetal Intestine Large	intestine
32	chr3:49906600-49907600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
33	chr3:49906600-49907600	Active TSS	H1 Cell Line	embryonic stem cell
34	chr3:49906600-49907600	Active TSS	iPS-20b Cell Line	embryonic stem cell
35	chr3:49906600-49907600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr3:49906600-49907600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
37	chr3:49906600-49907600	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
38	chr3:49906600-49907600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr3:49906600-49907600	Bivalent/Poised TSS	Psoas Muscle	Psoas
40	chr3:49906600-49907600	Flanking Bivalent TSS/Enh	Thymus	Thymus
41	chr3:49906600-49910800	Enhancers	Fetal Brain Male	brain
42	chr3:49906800-49907200	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
43	chr3:49906800-49907200	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
44	chr3:49906800-49907200	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
45	chr3:49906800-49907200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
46	chr3:49906800-49907200	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
47	chr3:49906800-49907200	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
48	chr3:49906800-49907200	Flanking Bivalent TSS/Enh	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr3:49906800-49907200	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
50	chr3:49906800-49907200	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin01	Skin

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