Variant report

Variant	rs3794376
Chromosome Location	chr13:50114491-50114492
allele	A/G
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	ELK1	chr13:50114461-50114647	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:50101816..50103530-chr13:50113861..50116343,2	K562	blood:

Variant related genes	Relation type
RCBTB1	TF binding region

Extended variants
information (count: 46 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1198422	0.90[JPT][hapmap]
rs1359542	0.86[EUR][1000 genomes]
rs1536192	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1536195	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1570883	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1570884	0.85[CEU][hapmap]
rs1886793	0.86[EUR][1000 genomes]
rs1977353	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1998780	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1998781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2104183	0.92[CEU][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes]
rs2146145	0.85[CEU][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes]
rs2274278	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2274284	1.00[CEU][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2407697	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2897741	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4941648	0.85[CEU][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.85[MKK][hapmap];0.96[TSI][hapmap];0.86[EUR][1000 genomes]
rs4941650	0.85[EUR][1000 genomes]
rs5007254	0.82[EUR][1000 genomes]
rs6561539	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6561540	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561542	0.92[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7139724	0.86[EUR][1000 genomes]
rs7317140	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7324024	0.85[CEU][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.85[MKK][hapmap];0.96[TSI][hapmap];0.86[EUR][1000 genomes]
rs7325207	0.89[EUR][1000 genomes]
rs7983283	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7986405	0.85[EUR][1000 genomes]
rs7989286	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7992396	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7992691	0.82[EUR][1000 genomes]
rs7996012	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs8000962	0.81[EUR][1000 genomes]
rs9526577	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9535259	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9535262	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9535269	0.85[EUR][1000 genomes]
rs9562896	0.82[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047311	chr13:49895019-50224227	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv916093	chr13:50050919-50290245	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1036135	chr13:50071310-50183103	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv541770	chr13:50071310-50183103	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv1054965	chr13:50102730-50251347	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv541771	chr13:50102730-50251347	Enhancers Active TSS Genic enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	esv2763020	chr13:50105055-50192259	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv900071	chr13:50107289-50286218	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3794376	CAB39L	cis	cerebellum	SCAN
rs3794376	RCBTB1	cis	cerebellum	SCAN
rs3794376	RCBTB1	cis	parietal	SCAN
rs3794376	ARL11	cis	parietal	SCAN
rs3794376	TBC1D22A	cis	Liver	GTEx
rs3794376	HSS00001599	trans	multi-tissue	Pritchard
rs3794376	PHF11	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50075000-50143800	Weak transcription	Small Intestine	intestine
2	chr13:50088400-50151000	Weak transcription	Psoas Muscle	Psoas
3	chr13:50088600-50134200	Weak transcription	Stomach Mucosa	stomach
4	chr13:50090000-50122800	Weak transcription	Ovary	ovary
5	chr13:50090000-50123600	Weak transcription	Esophagus	oesophagus
6	chr13:50090200-50117800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr13:50091400-50138800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr13:50094600-50120000	Weak transcription	Spleen	Spleen
9	chr13:50094600-50141600	Weak transcription	Right Ventricle	heart
10	chr13:50095000-50120400	Weak transcription	A549	lung
11	chr13:50097800-50135000	Weak transcription	Colonic Mucosa	Colon
12	chr13:50101600-50114600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr13:50101600-50142800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr13:50104600-50143800	Weak transcription	Hela-S3	cervix
15	chr13:50105400-50114600	Weak transcription	K562	blood
16	chr13:50105400-50114800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr13:50106600-50133200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr13:50108600-50158800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr13:50109200-50121600	Weak transcription	Brain Germinal Matrix	brain
20	chr13:50110400-50134400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr13:50110600-50114600	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr13:50110600-50124800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr13:50110800-50126800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr13:50111400-50114800	Weak transcription	Brain Hippocampus Middle	brain
25	chr13:50111400-50127600	Weak transcription	Fetal Heart	heart
26	chr13:50111600-50114600	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr13:50111600-50116000	Strong transcription	Fetal Muscle Trunk	muscle
28	chr13:50111600-50136600	Strong transcription	Dnd41	blood
29	chr13:50111800-50115400	Strong transcription	HSMM	muscle
30	chr13:50111800-50133200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr13:50112000-50118200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr13:50112000-50118400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr13:50112000-50135000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr13:50112200-50114600	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr13:50112200-50118200	Strong transcription	Fetal Muscle Leg	muscle
36	chr13:50112200-50121200	Strong transcription	Fetal Intestine Large	intestine
37	chr13:50112200-50134200	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr13:50112200-50138400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr13:50112400-50116600	Strong transcription	Fetal Stomach	stomach
40	chr13:50112400-50118200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr13:50112800-50114600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr13:50113000-50114600	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr13:50113200-50114600	Genic enhancers	HUVEC	blood vessel
44	chr13:50113200-50114800	Strong transcription	NHDF-Ad	bronchial
45	chr13:50113200-50115800	Strong transcription	HSMMtube	muscle
46	chr13:50113200-50116000	Strong transcription	HepG2	liver
47	chr13:50113200-50118200	Strong transcription	NHEK	skin
48	chr13:50113200-50121400	Strong transcription	HMEC	breast
49	chr13:50113200-50127200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr13:50113400-50114600	Enhancers	Primary T cells from cord blood	blood

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