Variant report

Variant	rs13015130
Chromosome Location	chr2:114034952-114034953
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	chr2:114033208..114035776-chr2:114039656..114042402,2	K562	blood:

Extended variants
information (count: 25 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1021409	0.88[ASN][1000 genomes]
rs11123176	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11123177	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11123179	0.85[AMR][1000 genomes]
rs11685107	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11685421	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11691437	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12471722	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12475140	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12476056	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12476331	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12478795	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12999288	0.88[ASN][1000 genomes]
rs1900216	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2002510	0.83[AMR][1000 genomes]
rs35006857	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4848321	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs877202	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs895416	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs895417	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs935365	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv508162	chr2:113983043-114099966	Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv535895	chr2:114015492-114037018	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv874901	chr2:114022569-114079565	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv998204	chr2:114023917-114075446	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs13015130	LOC654433	Cis_1M	lymphoblastoid	RTeQTL
rs13015130	PAX8	cis	lung	GTEx
rs13015130	AC016683.6	cis	Whole Blood	GTEx
rs13015130	PAX8	cis	Whole Blood	GTEx
rs13015130	AC016683.6	cis	lung	GTEx

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:114023200-114039800	Weak transcription	Gastric	stomach
2	chr2:114031600-114037000	Bivalent/Poised TSS	Fetal Kidney	kidney
3	chr2:114032600-114035000	Weak transcription	Right Atrium	heart
4	chr2:114032800-114035800	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
5	chr2:114033000-114035400	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
6	chr2:114033000-114035800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
7	chr2:114033000-114036600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
8	chr2:114033000-114038000	Weak transcription	A549	lung
9	chr2:114033200-114035000	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
10	chr2:114033200-114035000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr2:114033200-114035400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
12	chr2:114033200-114036000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
13	chr2:114033400-114035000	Bivalent Enhancer	Primary hematopoietic stem cells	blood
14	chr2:114033400-114035000	Bivalent Enhancer	Left Ventricle	heart
15	chr2:114033400-114035600	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr2:114033400-114035600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
17	chr2:114033400-114035600	Bivalent Enhancer	Spleen	Spleen
18	chr2:114033400-114036000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr2:114033400-114036000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
20	chr2:114033400-114036400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
21	chr2:114033400-114036400	Bivalent Enhancer	Fetal Brain Male	brain
22	chr2:114033400-114036600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
23	chr2:114033600-114036000	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
24	chr2:114033600-114036400	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr2:114033600-114036400	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr2:114033600-114037200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
27	chr2:114033800-114035400	Bivalent Enhancer	Stomach Mucosa	stomach
28	chr2:114034000-114036200	Transcr. at gene 5' and 3'	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr2:114034200-114036600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
30	chr2:114034200-114036600	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr2:114034400-114035000	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
32	chr2:114034400-114035200	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
33	chr2:114034400-114035200	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
34	chr2:114034400-114035400	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr2:114034400-114035400	Bivalent Enhancer	Brain Anterior Caudate	brain
36	chr2:114034400-114035600	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
37	chr2:114034400-114035600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr2:114034400-114035600	Enhancers	Pancreas	Pancrea
39	chr2:114034400-114035600	Bivalent Enhancer	NH-A	brain
40	chr2:114034400-114035800	Bivalent Enhancer	Esophagus	oesophagus
41	chr2:114034400-114035800	Flanking Bivalent TSS/Enh	Right Ventricle	heart
42	chr2:114034400-114036000	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
43	chr2:114034400-114036000	Bivalent Enhancer	Fetal Muscle Leg	muscle
44	chr2:114034400-114036200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
45	chr2:114034600-114035000	Bivalent Enhancer	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr2:114034600-114035000	Bivalent/Poised TSS	Primary T cells from cord blood	blood
47	chr2:114034600-114035000	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
48	chr2:114034600-114035000	Bivalent Enhancer	Adipose Nuclei	Adipose
49	chr2:114034600-114035200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr2:114034600-114035200	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links