Variant report

Variant	rs6542127
Chromosome Location	chr2:114022658-114022659
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10864911	0.84[EUR][1000 genomes]
rs10864912	0.92[CEU][hapmap];0.87[MEX][hapmap];0.85[EUR][1000 genomes]
rs11123173	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12990456	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13001920	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13429413	0.81[EUR][1000 genomes]
rs1374161	0.82[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.86[GIH][hapmap];0.93[JPT][hapmap];0.88[LWK][hapmap];0.83[MEX][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1446246	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs1466018	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1491584	0.87[JPT][hapmap]
rs1491585	0.92[JPT][hapmap];0.81[EUR][1000 genomes]
rs1491586	0.87[JPT][hapmap]
rs2121245	0.86[JPT][hapmap]
rs2863244	0.87[JPT][hapmap]
rs4142815	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4848323	0.85[CEU][hapmap];0.87[MEX][hapmap]
rs4849188	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6720637	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6726151	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6734610	0.82[ASW][hapmap];0.88[CEU][hapmap];0.89[CHB][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];0.93[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6753216	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs708633	0.82[CEU][hapmap]
rs7560701	0.94[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.99[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs895415	0.82[CEU][hapmap]
rs895418	0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[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	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	nsv535895	chr2:114015492-114037018	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	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

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs6542127	AC016683.6	cis	Artery Tibial	GTEx
rs6542127	AC016683.6	cis	Adipose Subcutaneous	GTEx
rs6542127	AC016683.6	cis	Muscle Skeletal	GTEx
rs6542127	PAX8	cis	Adipose Subcutaneous	GTEx
rs6542127	AC016683.6	cis	lung	GTEx
rs6542127	PAX8	cis	parietal	SCAN
rs6542127	LOC654433	cis	parietal	SCAN
rs6542127	PAX8	cis	lymphoblastoid	seeQTL
rs6542127	LOC654433	cis	cerebellum	SCAN
rs6542127	AC016683.6	cis	Esophagus Mucosa	GTEx
rs6542127	PAX8	cis	multi-tissue	Pritchard
rs6542127	AC016683.6	cis	Whole Blood	GTEx
rs6542127	PAX8	cis	Esophagus Mucosa	GTEx

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113999600-114028400	Weak transcription	Ovary	ovary
2	chr2:114010200-114030400	Weak transcription	GM12878-XiMat	blood
3	chr2:114015200-114022800	Weak transcription	Colon Smooth Muscle	Colon
4	chr2:114015800-114023600	Weak transcription	HSMM	muscle
5	chr2:114016200-114023600	Weak transcription	HSMMtube	muscle
6	chr2:114016200-114028000	Weak transcription	Fetal Brain Female	brain
7	chr2:114016400-114026000	Weak transcription	Fetal Heart	heart
8	chr2:114018800-114023800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr2:114019200-114024000	Weak transcription	Fetal Muscle Trunk	muscle
10	chr2:114019200-114026800	Weak transcription	Primary hematopoietic stem cells	blood
11	chr2:114019400-114028200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr2:114019600-114026000	Weak transcription	Spleen	Spleen
13	chr2:114020000-114027800	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr2:114020400-114023800	Enhancers	Liver	Liver
15	chr2:114020600-114023000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
16	chr2:114021000-114024200	Strong transcription	Placenta	Placenta
17	chr2:114021200-114024000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr2:114021200-114024000	Strong transcription	Lung	lung
19	chr2:114021200-114028200	Strong transcription	Duodenum Mucosa	Duodenum
20	chr2:114021400-114022800	Weak transcription	Fetal Muscle Leg	muscle
21	chr2:114021400-114023600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr2:114021400-114024800	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr2:114021600-114026200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr2:114021600-114028200	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr2:114021800-114024000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr2:114022000-114024600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr2:114022200-114023000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr2:114022200-114023400	Enhancers	Pancreas	Pancrea
29	chr2:114022200-114026400	Strong transcription	Primary T cells from cord blood	blood
30	chr2:114022200-114027600	Genic enhancers	Fetal Kidney	kidney
31	chr2:114022400-114023400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr2:114022400-114023800	Strong transcription	Adipose Nuclei	Adipose
33	chr2:114022400-114025000	Strong transcription	Fetal Thymus	thymus

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