Variant report

Variant	rs7979717
Chromosome Location	chr12:45242272-45242273
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10785539	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10880695	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10880696	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10880704	0.84[ASN][1000 genomes]
rs11182706	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11615964	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1506676	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1506678	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1506679	0.81[ASN][1000 genomes]
rs1506680	0.81[ASN][1000 genomes]
rs1876241	0.85[ASN][1000 genomes]
rs2465110	0.83[ASN][1000 genomes]
rs2658948	0.82[ASN][1000 genomes]
rs2658954	0.84[ASN][1000 genomes]
rs2939697	0.82[ASN][1000 genomes]
rs2939698	0.81[ASN][1000 genomes]
rs7295923	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7304472	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7305124	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7952764	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7953663	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7963606	0.81[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	esv3378050	chr12:44963059-45264289	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv832394	chr12:45077573-45269305	Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
3	nsv1036926	chr12:45131884-45273648	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
4	nsv541484	chr12:45131884-45273648	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7979717	DBX2	cis	Skin Sun Exposed Lower leg	GTEx
rs7979717	RP11-478B9.2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:45240200-45248400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
2	chr12:45240600-45242800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
3	chr12:45240800-45242400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
4	chr12:45240800-45242400	Enhancers	Thymus	Thymus
5	chr12:45240800-45242800	Enhancers	Primary B cells from peripheral blood	blood
6	chr12:45241000-45245200	Weak transcription	Colon Smooth Muscle	Colon
7	chr12:45241400-45242800	Flanking Active TSS	Dnd41	blood
8	chr12:45241600-45242400	Enhancers	Fetal Thymus	thymus
9	chr12:45241600-45242600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
10	chr12:45241800-45242400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
11	chr12:45241800-45242600	Flanking Active TSS	GM12878-XiMat	blood
12	chr12:45241800-45245800	Enhancers	Fetal Brain Male	brain
13	chr12:45242000-45242400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr12:45242000-45242400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr12:45242000-45242400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
16	chr12:45242000-45242400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
17	chr12:45242000-45242400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
18	chr12:45242000-45242400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr12:45242000-45242400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
20	chr12:45242000-45242400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
21	chr12:45242000-45242600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
22	chr12:45242000-45242800	Enhancers	iPS-15b Cell Line	embryonic stem cell
23	chr12:45242000-45242800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr12:45242000-45242800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
25	chr12:45242000-45243800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr12:45242200-45242400	Enhancers	Duodenum Mucosa	Duodenum
27	chr12:45242200-45242800	Enhancers	H1 Cell Line	embryonic stem cell
28	chr12:45242200-45242800	Enhancers	iPS-18 Cell Line	embryonic stem cell
29	chr12:45242200-45242800	Enhancers	Primary T cells fromperipheralblood	blood
30	chr12:45242200-45243800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr12:45242200-45244400	Enhancers	Fetal Brain Female	brain
32	chr12:45242200-45247400	Enhancers	Primary T cells from cord blood	blood

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