Variant report

Variant	rs3742291
Chromosome Location	chr13:52603775-52603776
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:52603093..52604723-chr13:52608557..52611141,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ATP7B-1	chr13:52603159-52603957	l_852_chr13:52603158-52624034_testes

Extended variants
information (count: 90 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs1004576	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1055062	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1060631	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1134727	0.90[ASN][1000 genomes]
rs12146904	0.90[ASN][1000 genomes]
rs12431310	0.90[ASN][1000 genomes]
rs12560598	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1571189	0.84[ASN][1000 genomes]
rs1886538	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1886539	0.88[ASN][1000 genomes]
rs1886543	0.90[ASN][1000 genomes]
rs1886544	0.90[ASN][1000 genomes]
rs1886545	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1886546	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2005182	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2147359	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2147360	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2147361	0.84[ASN][1000 genomes]
rs2277448	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2296347	0.88[ASN][1000 genomes]
rs2408546	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2408547	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2408548	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2408552	0.89[ASN][1000 genomes]
rs2408554	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2897964	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2897965	0.86[ASN][1000 genomes]
rs3742289	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3783242	0.90[ASN][1000 genomes]
rs3818422	0.90[ASN][1000 genomes]
rs4261421	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4264295	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4600369	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4941720	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4941723	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4941727	0.85[ASN][1000 genomes]
rs4943060	0.86[ASN][1000 genomes]
rs61958804	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61958805	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6561656	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6650384	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6650385	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66849828	0.85[ASN][1000 genomes]
rs7318287	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7319784	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7320252	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7320429	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs732071	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7320831	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7321120	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7321310	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7321435	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7321775	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7324458	0.90[ASN][1000 genomes]
rs7332272	0.82[ASN][1000 genomes]
rs7332356	0.90[ASN][1000 genomes]
rs7338131	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7998770	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9526817	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9526823	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526825	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9526826	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9526834	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9526835	0.86[ASN][1000 genomes]
rs9526836	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9526841	0.88[ASN][1000 genomes]
rs9526843	0.88[ASN][1000 genomes]
rs9535813	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9535816	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9535821	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9535824	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9535825	0.84[ASN][1000 genomes]
rs9535845	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9535853	0.90[ASN][1000 genomes]
rs9535861	0.82[ASN][1000 genomes]
rs9535867	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9535871	0.86[ASN][1000 genomes]
rs9535873	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9535883	0.81[ASN][1000 genomes]
rs9535889	0.84[ASN][1000 genomes]
rs9568682	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9568684	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9568692	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530718	chr13:52291802-52832752	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv1044310	chr13:52321564-52643924	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv1050117	chr13:52325116-52643924	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv934070	chr13:52362588-53174923	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Strong transcription Flanking 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	59 gene(s)	inside rSNPs	diseases
5	nsv900082	chr13:52555288-52709938	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv1040931	chr13:52564792-53350914	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
7	nsv541773	chr13:52564792-53350914	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3742291	ALG11	cis	Muscle Skeletal	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52588000-52609200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr13:52588000-52617400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr13:52589400-52605200	Strong transcription	Fetal Muscle Trunk	muscle
4	chr13:52589800-52605400	Strong transcription	Fetal Thymus	thymus
5	chr13:52590000-52604400	Strong transcription	Primary T cells from cord blood	blood
6	chr13:52590600-52604200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr13:52591000-52604600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr13:52591600-52604000	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr13:52591800-52603800	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr13:52593800-52604200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr13:52593800-52604400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr13:52593800-52604600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr13:52595000-52611200	Weak transcription	Psoas Muscle	Psoas
14	chr13:52595600-52605000	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr13:52595600-52606600	Weak transcription	Brain Angular Gyrus	brain
16	chr13:52596600-52614000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr13:52598000-52604000	Strong transcription	Primary B cells from peripheral blood	blood
18	chr13:52598000-52604400	Strong transcription	H1 Cell Line	embryonic stem cell
19	chr13:52598000-52604400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr13:52598200-52605400	Strong transcription	HSMM	muscle
21	chr13:52598200-52605600	Strong transcription	Fetal Brain Female	brain
22	chr13:52598200-52606000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr13:52598800-52604600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr13:52598800-52606600	Weak transcription	Rectal Smooth Muscle	rectum
25	chr13:52599000-52606400	Weak transcription	Brain Substantia Nigra	brain
26	chr13:52599000-52611000	Weak transcription	Fetal Brain Male	brain
27	chr13:52599200-52604600	Weak transcription	Fetal Heart	heart
28	chr13:52599200-52604600	ZNF genes & repeats	Fetal Muscle Leg	muscle
29	chr13:52599400-52603800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr13:52599400-52604400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
31	chr13:52599400-52604600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr13:52599600-52604000	Weak transcription	Spleen	Spleen
33	chr13:52599600-52604400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr13:52599600-52605000	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr13:52599800-52605800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr13:52600000-52604600	ZNF genes & repeats	Fetal Intestine Small	intestine
37	chr13:52600000-52605200	ZNF genes & repeats	Fetal Stomach	stomach
38	chr13:52600000-52609800	Weak transcription	Stomach Mucosa	stomach
39	chr13:52600200-52604000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr13:52600200-52613800	Weak transcription	Colon Smooth Muscle	Colon
41	chr13:52600200-52613800	Weak transcription	Small Intestine	intestine
42	chr13:52600400-52605000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr13:52600400-52627600	Weak transcription	HSMMtube	muscle
44	chr13:52600600-52604600	Weak transcription	Colonic Mucosa	Colon
45	chr13:52600800-52604200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr13:52600800-52606600	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr13:52600800-52609600	Weak transcription	Esophagus	oesophagus
48	chr13:52600800-52611400	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr13:52601000-52619400	Weak transcription	Brain Hippocampus Middle	brain
50	chr13:52601200-52603800	Weak transcription	Sigmoid Colon	Sigmoid Colon

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