Variant report

Variant	rs3015002
Chromosome Location	chr12:68404633-68404634
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1019076	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10878723	0.83[CEU][hapmap];0.81[JPT][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11177002	0.83[CEU][hapmap];0.81[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12582272	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1468487	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17104682	0.97[GIH][hapmap];0.87[TSI][hapmap]
rs2051993	0.81[EUR][1000 genomes]
rs2159064	0.93[EUR][1000 genomes]
rs2860609	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2906854	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2906856	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2906859	0.83[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2906862	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3015001	0.83[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs61923060	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7306466	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7952790	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7962511	0.83[CEU][hapmap];0.81[JPT][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3411149	chr12:68066948-68435533	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv975509	chr12:68382193-68405026	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3015002	FRS2	cis	parietal	SCAN
rs3015002	IFNG-AS1	cis	Artery Tibial	GTEx
rs3015002	CPM	cis	parietal	SCAN
rs3015002	IFNG-AS1	cis	Whole Blood	GTEx
rs3015002	IFNG-AS1	cis	Muscle Skeletal	GTEx
rs3015002	SLC35E3	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:68391400-68405400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr12:68392400-68404800	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr12:68392600-68413800	Weak transcription	Primary T cells from cord blood	blood
4	chr12:68392800-68405200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr12:68393000-68405000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr12:68397200-68405400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr12:68398400-68405400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr12:68398400-68422200	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr12:68399200-68404800	Weak transcription	Primary B cells from peripheral blood	blood
10	chr12:68401000-68405400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr12:68401200-68405400	Weak transcription	HSMMtube	muscle
12	chr12:68401600-68405400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr12:68401800-68405200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr12:68402000-68405400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr12:68404200-68405000	Strong transcription	Primary B cells from cord blood	blood
16	chr12:68404200-68405400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr12:68404200-68406400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr12:68404400-68405400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr12:68404400-68407000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr12:68404600-68404800	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr12:68404600-68406000	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr12:68404600-68406400	Enhancers	Primary T killer memory cells from peripheral blood	blood

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