Variant report

Variant	rs7952790
Chromosome Location	chr12:68406452-68406453
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	chr12:68405131..68407341-chr12:68430769..68432626,2	K562	blood:

Extended variants
information (count: 23 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1019076	0.81[EUR][1000 genomes]
rs10878723	0.90[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.88[MEX][hapmap];0.80[MKK][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10878726	0.86[ASN][1000 genomes]
rs11177002	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11177008	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12228471	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12582272	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1468487	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17104682	0.90[ASW][hapmap];0.95[CEU][hapmap];0.82[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2051993	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2860609	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2870960	0.94[CEU][hapmap];0.84[JPT][hapmap];0.85[YRI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2906854	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2906856	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2906859	1.00[CEU][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2906862	0.82[CEU][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3015001	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3015002	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56393928	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61923060	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7306466	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7962511	0.90[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7952790	FRS2	cis	parietal	SCAN
rs7952790	IFNG-AS1	cis	Artery Tibial	GTEx
rs7952790	CPM	cis	parietal	SCAN
rs7952790	IFNG-AS1	cis	Muscle Skeletal	GTEx
rs7952790	IFNG-AS1	cis	Whole Blood	GTEx

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:68392600-68413800	Weak transcription	Primary T cells from cord blood	blood
2	chr12:68398400-68422200	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr12:68404400-68407000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr12:68404800-68407800	Enhancers	Primary B cells from peripheral blood	blood
5	chr12:68405200-68407200	Enhancers	Primary T helper cells fromperipheralblood	blood
6	chr12:68405200-68407400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr12:68405400-68406800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr12:68405400-68407200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr12:68405400-68407200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr12:68405400-68407600	Enhancers	Primary B cells from cord blood	blood
11	chr12:68405400-68407600	Enhancers	HSMMtube	muscle
12	chr12:68405400-68408000	Enhancers	Dnd41	blood
13	chr12:68405600-68407000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr12:68405800-68407400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr12:68406000-68406800	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr12:68406000-68406800	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr12:68406000-68407200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr12:68406000-68407200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr12:68406000-68425200	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr12:68406200-68407000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr12:68406200-68407000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr12:68406200-68407000	Enhancers	NHDF-Ad	bronchial
23	chr12:68406200-68407200	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr12:68406200-68407400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr12:68406200-68411800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr12:68406200-68413800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr12:68406400-68407400	Enhancers	HSMM	muscle
28	chr12:68406400-68426000	Weak transcription	Primary T cells fromperipheralblood	blood

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