Variant report

Variant	rs2330150
Chromosome Location	chr5:43299600-43299601
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	chr5:43299532-43299761	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:43296533..43300928-chr5:43302565..43304605,4	K562	blood:
2	chr5:43296533..43300517-chr5:43302565..43304936,4	K562	blood:
3	chr5:43299389..43301701-chr5:43312894..43314825,2	K562	blood:

Variant related genes	Relation type
HMGCS1	TF binding region
ENSG00000112972	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10039048	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10039617	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10512825	0.85[EUR][1000 genomes]
rs10805671	0.81[EUR][1000 genomes]
rs10805672	0.85[EUR][1000 genomes]
rs10941621	0.85[EUR][1000 genomes]
rs10941622	0.85[EUR][1000 genomes]
rs10941623	0.85[EUR][1000 genomes]
rs10941628	0.81[EUR][1000 genomes]
rs11739009	0.82[EUR][1000 genomes]
rs11739665	0.85[EUR][1000 genomes]
rs11741246	0.81[EUR][1000 genomes]
rs11742712	0.82[EUR][1000 genomes]
rs11743622	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11747105	0.81[EUR][1000 genomes]
rs11747834	0.81[EUR][1000 genomes]
rs12189016	0.81[EUR][1000 genomes]
rs12514393	0.83[EUR][1000 genomes]
rs12514399	0.83[EUR][1000 genomes]
rs12515072	0.85[EUR][1000 genomes]
rs12518032	0.85[EUR][1000 genomes]
rs12520012	0.85[EUR][1000 genomes]
rs12522178	0.81[EUR][1000 genomes]
rs13161494	0.83[ASN][1000 genomes]
rs13187876	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13659	0.84[EUR][1000 genomes]
rs1545753	0.84[EUR][1000 genomes]
rs1548097	0.85[EUR][1000 genomes]
rs1564198	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2126947	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2126948	0.82[EUR][1000 genomes]
rs2126949	0.82[EUR][1000 genomes]
rs2169781	0.83[EUR][1000 genomes]
rs2330243	0.83[ASN][1000 genomes]
rs35239179	0.85[EUR][1000 genomes]
rs3733768	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3733769	0.85[EUR][1000 genomes]
rs4373285	0.85[EUR][1000 genomes]
rs4395639	0.80[EUR][1000 genomes]
rs4443425	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4591755	0.81[EUR][1000 genomes]
rs4866734	0.80[EUR][1000 genomes]
rs4866737	0.82[EUR][1000 genomes]
rs4866738	0.82[EUR][1000 genomes]
rs4866741	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4866813	0.85[EUR][1000 genomes]
rs4866820	0.83[EUR][1000 genomes]
rs4866826	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55634155	0.82[EUR][1000 genomes]
rs55794239	0.84[EUR][1000 genomes]
rs56029402	0.80[EUR][1000 genomes]
rs56114604	0.85[EUR][1000 genomes]
rs57392430	0.80[EUR][1000 genomes]
rs57401732	0.82[EUR][1000 genomes]
rs58679159	0.82[EUR][1000 genomes]
rs59078439	0.80[EUR][1000 genomes]
rs60207549	0.81[ASN][1000 genomes]
rs60445501	0.82[EUR][1000 genomes]
rs6451684	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66691321	0.85[EUR][1000 genomes]
rs66914803	0.82[EUR][1000 genomes]
rs67415672	0.80[EUR][1000 genomes]
rs67497876	0.83[EUR][1000 genomes]
rs67651757	0.81[EUR][1000 genomes]
rs67817333	0.83[EUR][1000 genomes]
rs6814	0.84[EUR][1000 genomes]
rs6863360	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6895805	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6898398	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7445066	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7701391	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7704588	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7714919	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7716091	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7720165	0.85[EUR][1000 genomes]
rs7722781	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9292871	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9292874	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9790987	0.85[EUR][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	nsv1023741	chr5:42768215-43348145	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
2	nsv537737	chr5:42768215-43348145	Genic enhancers Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
3	nsv508352	chr5:43237830-43391062	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2330150	NNT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:128 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43284200-43309400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr5:43285000-43300800	Strong transcription	Cortex derived primary cultured neurospheres	brain
3	chr5:43285600-43300000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr5:43285600-43302000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr5:43285600-43302800	Strong transcription	Duodenum Mucosa	Duodenum
6	chr5:43286200-43300600	Strong transcription	Fetal Intestine Large	intestine
7	chr5:43286400-43302200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr5:43286400-43302400	Strong transcription	GM12878-XiMat	blood
9	chr5:43286600-43300400	Strong transcription	Fetal Thymus	thymus
10	chr5:43286600-43300800	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr5:43286600-43301000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr5:43286600-43301400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr5:43286600-43303000	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr5:43286600-43303000	Strong transcription	Primary hematopoietic stem cells	blood
15	chr5:43286800-43300000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr5:43286800-43300400	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr5:43286800-43300400	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr5:43286800-43301000	Strong transcription	K562	blood
19	chr5:43286800-43301400	Strong transcription	Primary T helper cells PMA-I stimulated	--
20	chr5:43286800-43301800	Strong transcription	HMEC	breast
21	chr5:43286800-43302400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr5:43286800-43302600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr5:43286800-43302600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr5:43286800-43304400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr5:43287000-43302800	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr5:43287000-43305000	Strong transcription	HUVEC	blood vessel
27	chr5:43287200-43301000	Strong transcription	Primary B cells from peripheral blood	blood
28	chr5:43287400-43300800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr5:43287400-43302600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
30	chr5:43287400-43302800	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr5:43287600-43302000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr5:43287800-43300600	Strong transcription	HepG2	liver
33	chr5:43287800-43303600	Strong transcription	H9 Cell Line	embryonic stem cell
34	chr5:43288200-43312400	Weak transcription	Spleen	Spleen
35	chr5:43288600-43310000	Weak transcription	Aorta	Aorta
36	chr5:43288800-43303600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr5:43289600-43303800	Strong transcription	Primary B cells from cord blood	blood
38	chr5:43289800-43300800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr5:43290400-43302400	Strong transcription	Primary T cells from cord blood	blood
40	chr5:43291000-43300400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr5:43291400-43301800	Weak transcription	Small Intestine	intestine
42	chr5:43291600-43301000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr5:43291600-43302800	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr5:43292000-43300600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr5:43292000-43301000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr5:43294200-43302800	Weak transcription	Pancreas	Pancrea
47	chr5:43294200-43303400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr5:43294200-43312400	Weak transcription	Thymus	Thymus
49	chr5:43294600-43309400	Weak transcription	Lung	lung
50	chr5:43294800-43299600	Strong transcription	NH-A	brain

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