Variant report

Variant	rs12620738
Chromosome Location	chr2:113963739-113963740
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	chr2:113836433..113838367-chr2:113961484..113963853,2	MCF-7	breast:
2	chr2:113941683..113943578-chr2:113962080..113965025,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PSD4-2	chr2:113963503-113966973	NONHSAT073752

Variant related genes	Relation type
ENSG00000125637	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10175462	0.85[ASN][1000 genomes]
rs10206269	0.84[ASN][1000 genomes]
rs1110839	0.86[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs11123170	0.95[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs11123172	0.95[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs12612729	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12619508	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2015769	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2019137	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2241978	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2276561	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2305133	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2863243	0.85[ASN][1000 genomes]
rs3748916	0.87[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.83[YRI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3811059	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3828188	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3828189	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4848318	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4849169	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4849176	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4849177	0.95[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs4849179	0.95[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs4849181	0.81[ASN][1000 genomes]
rs4849183	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62160781	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6707386	0.85[ASN][1000 genomes]
rs6751201	0.89[JPT][hapmap]
rs6755040	0.85[ASN][1000 genomes]
rs6755639	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs731834	0.87[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7421852	0.84[ASN][1000 genomes]
rs7563094	0.85[ASN][1000 genomes]
rs7578633	0.85[ASN][1000 genomes]
rs7589901	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs874898	0.94[JPT][hapmap]
rs895412	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs902695	0.87[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs902696	0.87[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[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	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
4	nsv874900	chr2:113948378-113967990	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs12620738	LOC654433	cis	cerebellum	SCAN
rs12620738	AC016683.6	cis	Muscle Skeletal	GTEx
rs12620738	PAX8	cis	Esophagus Mucosa	GTEx
rs12620738	AC016683.6	cis	Esophagus Muscularis	GTEx
rs12620738	PAX8	cis	lymphoblastoid	seeQTL
rs12620738	PAX8	cis	parietal	SCAN
rs12620738	LOC654433	Cis_1M	lymphoblastoid	RTeQTL
rs12620738	LOC654433	cis	parietal	SCAN
rs12620738	AC016683.6	cis	Artery Tibial	GTEx
rs12620738	PAX8	cis	Adipose Subcutaneous	GTEx
rs12620738	AC016683.6	cis	Nerve Tibial	GTEx
rs12620738	AC016683.6	cis	lung	GTEx
rs12620738	AC016683.6	cis	Adipose Subcutaneous	GTEx
rs12620738	PAX8	cis	Esophagus Muscularis	GTEx
rs12620738	AC016683.6	cis	Whole Blood	GTEx
rs12620738	AC016683.6	cis	Esophagus Mucosa	GTEx
rs12620738	PAX8	cis	lung	GTEx

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113957200-113969000	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr2:113957200-113969000	Weak transcription	Right Atrium	heart
3	chr2:113957400-113967000	Weak transcription	Stomach Smooth Muscle	stomach
4	chr2:113957400-113967800	Weak transcription	Adipose Nuclei	Adipose
5	chr2:113957400-113969000	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr2:113957400-113982600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr2:113958000-113975200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr2:113958200-113966400	Weak transcription	HSMMtube	muscle
9	chr2:113959000-113966600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr2:113959200-113968800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr2:113959200-113968800	Weak transcription	K562	blood
12	chr2:113959600-113967000	Weak transcription	Colonic Mucosa	Colon
13	chr2:113959600-113967600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr2:113960600-113963800	Weak transcription	Esophagus	oesophagus
15	chr2:113960600-113966200	Weak transcription	Fetal Stomach	stomach
16	chr2:113960600-113975200	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr2:113960800-113968600	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr2:113960800-113969600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr2:113960800-113974600	Weak transcription	Primary hematopoietic stem cells	blood
20	chr2:113960800-113975000	Weak transcription	Liver	Liver
21	chr2:113961000-113963800	Weak transcription	Placenta	Placenta
22	chr2:113961000-113966200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr2:113961000-113966200	Weak transcription	HSMM	muscle
24	chr2:113961000-113967200	Weak transcription	Thymus	Thymus
25	chr2:113961000-113968400	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr2:113961800-113966600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr2:113962000-113964000	Weak transcription	Fetal Kidney	kidney
28	chr2:113962000-113966200	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr2:113962000-113966400	Weak transcription	NH-A	brain
30	chr2:113962000-113966600	Weak transcription	Stomach Mucosa	stomach
31	chr2:113962000-113966600	Weak transcription	NHDF-Ad	bronchial
32	chr2:113962000-113969600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr2:113962200-113966200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr2:113962200-113966200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr2:113962200-113966400	Weak transcription	Hela-S3	cervix
36	chr2:113962200-113967000	Weak transcription	NHEK	skin
37	chr2:113962200-113967200	Weak transcription	HMEC	breast
38	chr2:113962200-113968400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr2:113962200-113969000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr2:113962200-113969400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr2:113962200-113974800	Weak transcription	GM12878-XiMat	blood
42	chr2:113962400-113963800	Weak transcription	HepG2	liver
43	chr2:113962400-113964000	Weak transcription	Fetal Intestine Small	intestine
44	chr2:113962400-113966600	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr2:113962400-113968800	Weak transcription	Fetal Thymus	thymus
46	chr2:113962600-113964400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr2:113962600-113974600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr2:113963400-113964200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
49	chr2:113963400-113964200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr2:113963400-113964400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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