Variant report

Variant	rs4142815
Chromosome Location	chr2:114009329-114009330
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11123173	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12990456	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13001920	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13429413	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1466018	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1491585	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2863244	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4849188	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6542127	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6726151	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6734610	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7560701	0.87[ASN][1000 genomes]
rs895418	0.88[EUR][1000 genomes];0.87[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:11)

SNP	Gene	Cis/trans	Tissue	Source
rs4142815	PAX8	cis	Esophagus Mucosa	GTEx
rs4142815	AC016683.6	cis	Whole Blood	GTEx
rs4142815	AC016683.6	cis	Artery Tibial	GTEx
rs4142815	AC016683.6	cis	Adipose Subcutaneous	GTEx
rs4142815	AC016683.6	cis	lung	GTEx
rs4142815	AC016683.6	cis	Muscle Skeletal	GTEx
rs4142815	LOC654433	Cis_1M	lymphoblastoid	RTeQTL
rs4142815	PAX8	cis	Adipose Subcutaneous	GTEx
rs4142815	AC016683.6	cis	Esophagus Mucosa	GTEx
rs4142815	AC016683.6	cis	Nerve Tibial	GTEx
rs4142815	PAX8	cis	Esophagus Muscularis	GTEx

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113998200-114020600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr2:113999000-114014800	Weak transcription	Colon Smooth Muscle	Colon
3	chr2:113999200-114009400	Weak transcription	Duodenum Mucosa	Duodenum
4	chr2:113999200-114013200	Weak transcription	Placenta	Placenta
5	chr2:113999400-114009400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr2:113999600-114013200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr2:113999600-114016400	Weak transcription	Fetal Stomach	stomach
8	chr2:113999600-114028400	Weak transcription	Ovary	ovary
9	chr2:114000200-114012000	Weak transcription	NHDF-Ad	bronchial
10	chr2:114000600-114011000	Weak transcription	Esophagus	oesophagus
11	chr2:114002400-114015400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:114004800-114010600	Weak transcription	Fetal Kidney	kidney
13	chr2:114006600-114012200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
14	chr2:114006600-114016200	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr2:114006600-114016200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr2:114006800-114015800	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr2:114007200-114010200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr2:114007200-114014800	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr2:114007200-114016800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr2:114007400-114009400	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr2:114007400-114009600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr2:114007400-114009600	Weak transcription	Fetal Muscle Leg	muscle
23	chr2:114007400-114009800	Weak transcription	Stomach Mucosa	stomach
24	chr2:114007400-114009800	Weak transcription	NHEK	skin
25	chr2:114008000-114010000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr2:114008000-114012000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
27	chr2:114008000-114013200	Weak transcription	HSMMtube	muscle
28	chr2:114008400-114010200	Enhancers	Primary hematopoietic stem cells	blood
29	chr2:114008400-114011400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
30	chr2:114008400-114012600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr2:114008400-114012800	Enhancers	Fetal Thymus	thymus
32	chr2:114008400-114016000	Enhancers	Primary T cells fromperipheralblood	blood
33	chr2:114008600-114010000	Flanking Active TSS	Primary T cells from cord blood	blood
34	chr2:114008600-114010200	Enhancers	Adipose Nuclei	Adipose
35	chr2:114008600-114010200	Enhancers	GM12878-XiMat	blood
36	chr2:114008600-114010400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr2:114008600-114012400	Weak transcription	A549	lung
38	chr2:114008800-114009400	Enhancers	Right Ventricle	heart
39	chr2:114008800-114010000	Enhancers	Primary B cells from peripheral blood	blood
40	chr2:114008800-114010000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
41	chr2:114008800-114010400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr2:114008800-114010800	Weak transcription	HSMM	muscle
43	chr2:114008800-114013200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr2:114009000-114009800	Weak transcription	Lung	lung
45	chr2:114009000-114009800	Weak transcription	Psoas Muscle	Psoas
46	chr2:114009000-114010000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr2:114009000-114010200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
48	chr2:114009000-114010600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr2:114009000-114010600	Weak transcription	HMEC	breast
50	chr2:114009000-114013000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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