Variant report

Variant	rs2863240
Chromosome Location	chr2:113970116-113970117
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:113968482..113971643-chr2:113991034..113994286,5	MCF-7	breast:
2	chr2:113031655..113033342-chr2:113967822..113970476,2	K562	blood:
3	chr2:113967701..113970551-chr2:113977130..113979448,2	K562	blood:
4	chr2:113923220..113926121-chr2:113970035..113971940,2	K562	blood:
5	chr2:113968914..113973967-chr2:113991743..113995400,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000188177	Chromatin interaction
ENSG00000189223	Chromatin interaction
ENSG00000125618	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs1015754	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11123169	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2289897	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs931472	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	nsv997348	chr2:113688093-113986508	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv582711	chr2:113895516-113984503	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh 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	15 gene(s)	inside rSNPs	diseases
3	nsv582712	chr2:113932431-113985170	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs2863240	PAX8	cis	Nerve Tibial	GTEx
rs2863240	PAX8	cis	Adipose Subcutaneous	GTEx
rs2863240	PAX8	cis	lung	GTEx
rs2863240	AC016683.6	cis	Muscle Skeletal	GTEx
rs2863240	PAX8	cis	Artery Tibial	GTEx
rs2863240	AC016683.6	cis	Nerve Tibial	GTEx
rs2863240	AC016683.6	cis	Esophagus Mucosa	GTEx
rs2863240	LOC654433	Cis_1M	lymphoblastoid	RTeQTL
rs2863240	PAX8	cis	Esophagus Mucosa	GTEx
rs2863240	AC016683.6	cis	Whole Blood	GTEx
rs2863240	AC016683.6	cis	lung	GTEx
rs2863240	AC016683.6	cis	Adipose Subcutaneous	GTEx
rs2863240	PAX8	cis	Whole Blood	GTEx
rs2863240	AC016683.6	cis	Artery Tibial	GTEx
rs2863240	AC016683.6	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113957400-113982600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr2:113958000-113975200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:113960600-113975200	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr2:113960800-113974600	Weak transcription	Primary hematopoietic stem cells	blood
5	chr2:113960800-113975000	Weak transcription	Liver	Liver
6	chr2:113962200-113974800	Weak transcription	GM12878-XiMat	blood
7	chr2:113962600-113974600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr2:113964000-113972800	Enhancers	Fetal Kidney	kidney
9	chr2:113966200-113970400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr2:113966200-113972000	Enhancers	Fetal Stomach	stomach
11	chr2:113967000-113970800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr2:113967200-113971400	Enhancers	Placenta	Placenta
13	chr2:113967400-113971200	Weak transcription	Thymus	Thymus
14	chr2:113967600-113975200	Weak transcription	Gastric	stomach
15	chr2:113968200-113970400	Enhancers	NHLF	lung
16	chr2:113968200-113970600	Enhancers	Left Ventricle	heart
17	chr2:113968200-113970800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr2:113968200-113970800	Enhancers	NHDF-Ad	bronchial
19	chr2:113968200-113973200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr2:113968200-113973200	Enhancers	HepG2	liver
21	chr2:113968400-113970600	Enhancers	NH-A	brain
22	chr2:113968400-113971800	Enhancers	Brain Germinal Matrix	brain
23	chr2:113968400-113972000	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr2:113968600-113970600	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr2:113968600-113971000	Enhancers	Fetal Muscle Leg	muscle
26	chr2:113968800-113970400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr2:113968800-113971200	Enhancers	Fetal Lung	lung
28	chr2:113968800-113971400	Enhancers	Fetal Muscle Trunk	muscle
29	chr2:113969000-113970400	Enhancers	Duodenum Smooth Muscle	Duodenum
30	chr2:113969000-113970400	Enhancers	Small Intestine	intestine
31	chr2:113969000-113970600	Enhancers	Fetal Intestine Large	intestine
32	chr2:113969000-113970600	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr2:113969000-113970800	Enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr2:113969000-113970800	Enhancers	Right Atrium	heart
35	chr2:113969000-113971200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr2:113969000-113971600	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr2:113969000-113971800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
38	chr2:113969200-113970200	Flanking Active TSS	Adipose Nuclei	Adipose
39	chr2:113969200-113970800	Enhancers	Fetal Brain Male	brain
40	chr2:113969400-113970800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
41	chr2:113969400-113974800	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr2:113969400-113975400	Weak transcription	Right Ventricle	heart
43	chr2:113969600-113970600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr2:113969600-113970600	Enhancers	HUES64 Cell Line	embryonic stem cell
45	chr2:113969600-113970600	Enhancers	Brain Hippocampus Middle	brain
46	chr2:113969600-113970600	Enhancers	Fetal Intestine Small	intestine
47	chr2:113969600-113970600	Enhancers	Stomach Smooth Muscle	stomach
48	chr2:113969600-113970800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr2:113969600-113970800	Enhancers	Fetal Brain Female	brain
50	chr2:113969600-113971000	Enhancers	Fetal Heart	heart

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