Variant report

Variant	rs62263602
Chromosome Location	chr3:50152491-50152492
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:50152078-50154242	HepG2	liver:	n/a	n/a
2	POLR2A	chr3:50152466-50154389	GM12878	blood:	n/a	n/a
3	POLR2A	chr3:50152368-50152637	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:50129704..50131638-chr3:50149642..50152823,3	K562	blood:
2	chr3:50150154..50152874-chr3:50153182..50156279,3	K562	blood:
3	chr3:50130138..50132585-chr3:50151323..50154093,2	K562	blood:

Variant related genes	Relation type
RBM5	TF binding region
ENSG00000003756	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1046956	1.00[ASN][1000 genomes]
rs1061474	0.83[AFR][1000 genomes]
rs1138536	0.85[AFR][1000 genomes]
rs13059311	1.00[ASN][1000 genomes]
rs13064381	1.00[ASN][1000 genomes]
rs13067082	1.00[ASN][1000 genomes]
rs13071931	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13091525	1.00[ASN][1000 genomes]
rs13095697	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13097720	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs14321	1.00[ASN][1000 genomes]
rs17225749	1.00[ASN][1000 genomes]
rs17304079	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2014004	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2189691	0.88[EUR][1000 genomes]
rs2526384	1.00[ASN][1000 genomes]
rs2526387	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2526397	1.00[ASN][1000 genomes]
rs2526398	1.00[ASN][1000 genomes]
rs2624826	0.85[AFR][1000 genomes]
rs2624833	1.00[ASN][1000 genomes]
rs2624841	1.00[ASN][1000 genomes]
rs2624846	0.84[EUR][1000 genomes]
rs35012435	1.00[ASN][1000 genomes]
rs35129566	1.00[ASN][1000 genomes]
rs35375092	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35491931	1.00[ASN][1000 genomes]
rs35849525	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55924524	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62260720	1.00[ASN][1000 genomes]
rs62260755	1.00[ASN][1000 genomes]
rs62262061	1.00[ASN][1000 genomes]
rs62262106	1.00[ASN][1000 genomes]
rs62262118	1.00[ASN][1000 genomes]
rs6787892	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7061	0.83[AFR][1000 genomes]
rs71326904	1.00[ASN][1000 genomes]
rs71326915	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7615318	1.00[ASN][1000 genomes]
rs7635601	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7648652	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7649428	1.00[ASN][1000 genomes]
rs9858297	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv460527	chr3:50028385-50153356	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv590249	chr3:50028385-50153356	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv834690	chr3:50101835-50267584	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers 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	24 gene(s)	inside rSNPs	diseases
5	nsv515986	chr3:50104307-50267584	Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Genic enhancers Flanking Active TSS 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	24 gene(s)	inside rSNPs	diseases
6	nsv432418	chr3:50114496-50224196	Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv1001775	chr3:50129479-50311666	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
8	nsv818139	chr3:50144951-50174572	Weak transcription Strong transcription Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv876768	chr3:50144951-50267584	Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
10	nsv523662	chr3:50144951-50584999	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
11	nsv1013949	chr3:50151712-50339163	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs62263602	BSN	cis	brain	BrainEAC
rs62263602	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs62263602	RBM6	cis	Artery Tibial	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50127800-50157800	Strong transcription	H9 Cell Line	embryonic stem cell
2	chr3:50128000-50152600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:50128000-50157800	Strong transcription	HUES48 Cell Line	embryonic stem cell
4	chr3:50128000-50158000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
5	chr3:50128000-50158000	Strong transcription	Fetal Muscle Trunk	muscle
6	chr3:50128200-50152800	Strong transcription	H1 Cell Line	embryonic stem cell
7	chr3:50128200-50158800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr3:50128400-50157800	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr3:50128400-50158200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr3:50128400-50158400	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr3:50128400-50159000	Strong transcription	Lung	lung
12	chr3:50128600-50156200	Strong transcription	Ovary	ovary
13	chr3:50128600-50158000	Strong transcription	NH-A	brain
14	chr3:50128600-50158400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr3:50128600-50158400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr3:50128600-50158600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr3:50128600-50158600	Strong transcription	Colonic Mucosa	Colon
18	chr3:50128600-50158800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr3:50128600-50158800	Strong transcription	Brain Germinal Matrix	brain
20	chr3:50128600-50158800	Strong transcription	Placenta Amnion	Placenta Amnion
21	chr3:50128600-50159000	Strong transcription	Brain Angular Gyrus	brain
22	chr3:50128600-50159000	Strong transcription	Placenta	Placenta
23	chr3:50128600-50159000	Strong transcription	Sigmoid Colon	Sigmoid Colon
24	chr3:50128600-50159200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr3:50128600-50159200	Strong transcription	Liver	Liver
26	chr3:50128600-50159200	Strong transcription	NHEK	skin
27	chr3:50128600-50160400	Strong transcription	Fetal Thymus	thymus
28	chr3:50128800-50156600	Strong transcription	Cortex derived primary cultured neurospheres	brain
29	chr3:50128800-50156600	Strong transcription	Brain Substantia Nigra	brain
30	chr3:50128800-50158600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr3:50128800-50158600	Strong transcription	HMEC	breast
32	chr3:50128800-50159000	Strong transcription	Brain Anterior Caudate	brain
33	chr3:50129000-50158600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr3:50129000-50158600	Strong transcription	Duodenum Mucosa	Duodenum
35	chr3:50129000-50158800	Strong transcription	Fetal Intestine Large	intestine
36	chr3:50129000-50159000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr3:50129000-50159200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr3:50129000-50159200	Strong transcription	Primary B cells from peripheral blood	blood
39	chr3:50129000-50159400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr3:50129000-50159400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr3:50129000-50160000	Strong transcription	Fetal Stomach	stomach
42	chr3:50129000-50160000	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr3:50129000-50160800	Strong transcription	Primary neutrophils fromperipheralblood	blood
44	chr3:50129200-50157600	Strong transcription	Primary T killer memory cells from peripheral blood	blood
45	chr3:50129200-50158600	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr3:50129200-50158800	Strong transcription	Primary B cells from cord blood	blood
47	chr3:50129200-50158800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr3:50129200-50158800	Strong transcription	Brain Hippocampus Middle	brain
49	chr3:50129200-50159000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr3:50129200-50159600	Strong transcription	Stomach Smooth Muscle	stomach

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