Variant report

Variant	rs13002606
Chromosome Location	chr2:114045382-114045383
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10201645	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10209795	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11123174	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11123175	0.87[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11679928	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11683025	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11687706	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11688620	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11889663	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12467534	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12989922	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13022812	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13385108	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13388160	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17626434	0.85[AMR][1000 genomes]
rs17626470	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34657362	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4091938	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4848324	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4848325	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4848326	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4848327	0.96[CEU][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4848328	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4848329	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4848330	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4849191	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4849192	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4849194	0.91[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6753679	0.89[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6760462	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6760648	0.85[EUR][1000 genomes]
rs7587376	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
3	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
4	nsv961872	chr2:114041837-114061641	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	esv2762785	chr2:114044712-114081784	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs13002606	PAX8	cis	lung	GTEx
rs13002606	PAX8	cis	lymphoblastoid	seeQTL
rs13002606	PAX8	cis	Esophagus Mucosa	GTEx
rs13002606	PAX8	cis	multi-tissue	Pritchard
rs13002606	AC016683.6	cis	Nerve Tibial	GTEx
rs13002606	PAX8	cis	parietal	SCAN
rs13002606	LOC654433	Cis_1M	lymphoblastoid	RTeQTL
rs13002606	PAX8	cis	Adipose Subcutaneous	GTEx
rs13002606	AC016683.6	cis	Whole Blood	GTEx
rs13002606	AC016683.6	cis	Esophagus Mucosa	GTEx
rs13002606	PAX8	cis	Esophagus Muscularis	GTEx
rs13002606	AC016683.6	cis	lung	GTEx
rs13002606	LOC654433	cis	cerebellum	SCAN
rs13002606	LOC654433	cis	parietal	SCAN
rs13002606	PAX8	cis	Nerve Tibial	GTEx
rs13002606	AC016683.6	cis	Muscle Skeletal	GTEx
rs13002606	AC016683.6	cis	Adipose Subcutaneous	GTEx
rs13002606	RP11-65I12.1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:114040600-114047000	Enhancers	Liver	Liver
2	chr2:114040600-114047800	Weak transcription	Gastric	stomach
3	chr2:114042200-114045400	Weak transcription	Stomach Mucosa	stomach
4	chr2:114042200-114046000	Weak transcription	Brain Anterior Caudate	brain
5	chr2:114042200-114046200	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr2:114042600-114048600	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr2:114043200-114048800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr2:114043400-114047800	Weak transcription	Lung	lung
9	chr2:114043600-114045400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr2:114043600-114045400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr2:114043600-114046000	Enhancers	HepG2	liver
12	chr2:114043600-114048600	Weak transcription	NHEK	skin
13	chr2:114043800-114045600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr2:114043800-114045800	Weak transcription	Stomach Smooth Muscle	stomach
15	chr2:114043800-114046000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr2:114043800-114048600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr2:114044200-114046400	Weak transcription	Pancreas	Pancrea
18	chr2:114044600-114049200	Enhancers	Fetal Intestine Small	intestine
19	chr2:114044800-114048600	Enhancers	Fetal Intestine Large	intestine
20	chr2:114045000-114046800	Enhancers	HMEC	breast
21	chr2:114045200-114045400	Enhancers	Duodenum Mucosa	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links