Variant report

Variant	rs13066173
Chromosome Location	chr3:42595839-42595840
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:42585374..42587081-chr3:42594734..42596739,2	K562	blood:
2	chr3:42595447..42597634-chr3:42622198..42624587,2	K562	blood:

Variant related genes	Relation type
ENSG00000093183	Chromatin interaction
ENSG00000008324	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs13064311	0.90[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13066333	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs168138	0.83[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.83[YRI][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs171057	0.92[ASN][1000 genomes]
rs2068278	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2271181	0.97[ASN][1000 genomes]
rs2271184	1.00[ASW][hapmap];0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.88[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2271187	0.83[ASW][hapmap];0.90[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.88[LWK][hapmap];0.83[MEX][hapmap];0.90[MKK][hapmap];0.86[TSI][hapmap];0.82[YRI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2284305	0.90[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs237064	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2940407	0.83[ASW][hapmap];0.90[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.86[LWK][hapmap];0.83[MEX][hapmap];0.88[MKK][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3095258	0.90[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.86[LWK][hapmap];0.83[MEX][hapmap];0.86[MKK][hapmap];0.84[ASN][1000 genomes]
rs339656	0.94[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.83[YRI][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs339720	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap]
rs339721	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap];0.81[ASN][1000 genomes]
rs339724	0.83[ASW][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap]
rs339729	0.94[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.83[YRI][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs339735	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs342523	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs342524	0.94[ASN][1000 genomes]
rs342525	0.92[ASN][1000 genomes]
rs342526	0.96[ASN][1000 genomes]
rs342534	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs342535	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs342538	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs383937	0.90[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs3888651	0.90[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs398743	0.94[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.86[YRI][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60994254	0.82[ASN][1000 genomes]
rs612362	0.90[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap]
rs637852	0.90[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.85[MKK][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs638904	0.85[ASN][1000 genomes]
rs651180	0.82[ASW][hapmap];0.90[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.88[LWK][hapmap];0.83[MEX][hapmap];0.83[MKK][hapmap];0.82[YRI][hapmap];0.84[ASN][1000 genomes]
rs654761	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs663258	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs664813	0.90[EUR][1000 genomes]
rs665206	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6799021	0.90[ASN][1000 genomes]
rs704982	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs807863	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs82755	0.83[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9311323	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9311324	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9813479	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9819563	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9828279	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005533	chr3:41953873-42596375	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1002944	chr3:42559762-42728909	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13066173	NKTR	cis	parietal	SCAN
rs13066173	SEC22C	Cis_1M	lymphoblastoid	RTeQTL
rs13066173	NKTR	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42577800-42597600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:42587000-42602400	Weak transcription	Colonic Mucosa	Colon
3	chr3:42587400-42597000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:42587400-42597200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr3:42587400-42606800	Weak transcription	Small Intestine	intestine
6	chr3:42587800-42597000	Strong transcription	Fetal Thymus	thymus
7	chr3:42587800-42597000	Strong transcription	Thymus	Thymus
8	chr3:42587800-42611800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr3:42588000-42613000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:42588400-42613000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr3:42588600-42618000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr3:42589000-42611800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr3:42589200-42611000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr3:42589400-42596800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr3:42589400-42610800	Weak transcription	Stomach Mucosa	stomach
16	chr3:42589400-42611000	Strong transcription	Fetal Stomach	stomach
17	chr3:42589400-42612400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr3:42589400-42614000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr3:42589600-42611200	Strong transcription	Fetal Intestine Small	intestine
20	chr3:42589600-42611800	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr3:42589800-42597000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr3:42589800-42597000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr3:42589800-42597200	Weak transcription	Hela-S3	cervix
24	chr3:42589800-42610600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr3:42589800-42611000	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr3:42589800-42616400	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr3:42590000-42597000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr3:42590000-42597800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr3:42590000-42598600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr3:42590000-42603800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr3:42590000-42611600	Strong transcription	Duodenum Mucosa	Duodenum
32	chr3:42590000-42612600	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr3:42590200-42601600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr3:42590200-42611600	Strong transcription	Fetal Muscle Leg	muscle
35	chr3:42590200-42611800	Strong transcription	Adipose Nuclei	Adipose
36	chr3:42590400-42597000	Strong transcription	Dnd41	blood
37	chr3:42590600-42597600	Strong transcription	GM12878-XiMat	blood
38	chr3:42590800-42599800	Strong transcription	HUVEC	blood vessel
39	chr3:42591000-42596000	Strong transcription	Primary hematopoietic stem cells	blood
40	chr3:42591000-42605400	Strong transcription	Left Ventricle	heart
41	chr3:42591000-42609200	Strong transcription	Fetal Intestine Large	intestine
42	chr3:42591000-42614000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr3:42591200-42596800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr3:42591200-42597600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr3:42591200-42610400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr3:42591200-42611800	Strong transcription	HUES6 Cell Line	embryonic stem cell
47	chr3:42591400-42611200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr3:42591600-42609400	Strong transcription	Primary B cells from cord blood	blood
49	chr3:42591600-42611800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr3:42591800-42609400	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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