Variant report

Variant	rs1021409
Chromosome Location	chr2:114008170-114008171
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11691437	0.88[ASN][1000 genomes]
rs12467324	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12471722	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12476331	0.88[ASN][1000 genomes]
rs12478795	0.88[ASN][1000 genomes]
rs12998725	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13015130	0.88[ASN][1000 genomes]
rs1900216	0.88[ASN][1000 genomes]
rs2003986	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35006857	0.88[ASN][1000 genomes]
rs3738913	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4848320	0.81[AMR][1000 genomes]
rs4848321	0.88[ASN][1000 genomes]
rs4849186	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs745912	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs877202	0.88[ASN][1000 genomes]
rs895416	0.88[ASN][1000 genomes]
rs895417	0.88[ASN][1000 genomes]
rs935365	0.88[ASN][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	nsv459008	chr2:113972945-114010791	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv582713	chr2:113972945-114010791	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1021409	PAX8	cis	lung	GTEx
rs1021409	LOC654433	Cis_1M	lymphoblastoid	RTeQTL
rs1021409	AC016683.6	cis	Whole Blood	GTEx
rs1021409	AC016683.6	cis	lung	GTEx

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113995600-114008600	Weak transcription	GM12878-XiMat	blood
2	chr2:113998200-114020600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr2:113999000-114014800	Weak transcription	Colon Smooth Muscle	Colon
4	chr2:113999200-114009400	Weak transcription	Duodenum Mucosa	Duodenum
5	chr2:113999200-114013200	Weak transcription	Placenta	Placenta
6	chr2:113999400-114009400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr2:113999600-114013200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr2:113999600-114016400	Weak transcription	Fetal Stomach	stomach
9	chr2:113999600-114028400	Weak transcription	Ovary	ovary
10	chr2:114000200-114009200	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr2:114000200-114012000	Weak transcription	NHDF-Ad	bronchial
12	chr2:114000600-114011000	Weak transcription	Esophagus	oesophagus
13	chr2:114002400-114015400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:114003600-114008400	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr2:114004200-114008800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr2:114004800-114010600	Weak transcription	Fetal Kidney	kidney
17	chr2:114005600-114008600	Weak transcription	Lung	lung
18	chr2:114006000-114008800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr2:114006400-114009000	Enhancers	HMEC	breast
20	chr2:114006600-114008600	Enhancers	A549	lung
21	chr2:114006600-114008800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr2:114006600-114008800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr2:114006600-114009000	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr2:114006600-114009000	Enhancers	K562	blood
25	chr2:114006600-114009200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr2:114006600-114012200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
27	chr2:114006600-114016200	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr2:114006600-114016200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr2:114006800-114008600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr2:114006800-114009200	Enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr2:114006800-114015800	Enhancers	Primary T helper cells fromperipheralblood	blood
32	chr2:114007000-114008400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr2:114007000-114008600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr2:114007000-114008600	Enhancers	Primary T cells from cord blood	blood
35	chr2:114007000-114008600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr2:114007000-114008600	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr2:114007000-114009200	Enhancers	HepG2	liver
38	chr2:114007200-114008200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr2:114007200-114008400	Weak transcription	Fetal Thymus	thymus
40	chr2:114007200-114008600	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr2:114007200-114008600	Weak transcription	Fetal Intestine Small	intestine
42	chr2:114007200-114008600	Weak transcription	Fetal Muscle Trunk	muscle
43	chr2:114007200-114008800	Weak transcription	Primary B cells from peripheral blood	blood
44	chr2:114007200-114009200	Weak transcription	Thymus	Thymus
45	chr2:114007200-114010200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr2:114007200-114014800	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr2:114007200-114016800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr2:114007400-114008400	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr2:114007400-114008400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr2:114007400-114008400	Weak transcription	HSMM	muscle

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