Variant report

Variant	rs12534918
Chromosome Location	chr7:127617772-127617773
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10487499	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10487502	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12154492	0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12155421	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12375023	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12531847	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12532894	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12533765	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12537331	0.85[GIH][hapmap];1.00[MEX][hapmap]
rs12540357	1.00[ASN][1000 genomes]
rs12706816	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12706818	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12706819	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12706820	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12706821	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12706822	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12706823	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13227201	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13229973	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13231367	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13238924	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13246200	0.89[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13246286	0.89[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1345283	1.00[ASN][1000 genomes]
rs1348103	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1362898	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1419970	0.89[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1468701	0.86[EUR][1000 genomes]
rs17151466	0.81[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17151488	0.89[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17151507	0.89[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17151639	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs17151653	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17151668	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17151682	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17151707	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17151739	0.85[GIH][hapmap];0.93[MEX][hapmap]
rs17676654	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34026100	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34688920	1.00[ASN][1000 genomes]
rs35154268	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41464647	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap]
rs55660321	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58489175	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6467157	0.89[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];0.88[LWK][hapmap];0.93[MEX][hapmap];0.86[TSI][hapmap];0.85[YRI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67827668	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6948605	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6953231	0.89[CEU][hapmap];1.00[CHB][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6959487	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6962635	0.89[ASW][hapmap];0.83[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73232968	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73232972	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73238078	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73238088	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73239704	0.81[AMR][1000 genomes]
rs741094	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7458839	0.85[EUR][1000 genomes]
rs7785596	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7805021	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7809182	0.89[CEU][hapmap];0.85[GIH][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs7810024	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9649027	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9649512	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][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	nsv1022385	chr7:127246656-127971194	Weak transcription Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv539120	chr7:127246656-127971194	Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv1016143	chr7:127251359-127726762	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv526535	chr7:127445594-127623840	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1024743	chr7:127498695-127670004	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12534918	C7orf54	cis	brain	BrainEAC

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:127570800-127618200	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr7:127571400-127617800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr7:127571600-127618000	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr7:127583200-127630600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr7:127584600-127617800	Weak transcription	Hela-S3	cervix
6	chr7:127587400-127618000	Weak transcription	NHLF	lung
7	chr7:127587400-127635200	Weak transcription	NHDF-Ad	bronchial
8	chr7:127594000-127623400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr7:127594400-127618000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr7:127594600-127618000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr7:127600000-127617800	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr7:127600400-127617800	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr7:127600400-127617800	Weak transcription	Primary hematopoietic stem cells	blood
14	chr7:127600400-127618200	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr7:127600600-127617800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr7:127600600-127630600	Weak transcription	Adipose Nuclei	Adipose
17	chr7:127603000-127627000	Weak transcription	Aorta	Aorta
18	chr7:127603200-127619200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr7:127603400-127619000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr7:127606400-127618000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr7:127607400-127624000	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr7:127607800-127626800	Weak transcription	Ovary	ovary
23	chr7:127609200-127618200	Weak transcription	Osteobl	bone
24	chr7:127609200-127618800	Weak transcription	Fetal Thymus	thymus
25	chr7:127609200-127630800	Weak transcription	NH-A	brain
26	chr7:127609400-127623400	Weak transcription	Pancreas	Pancrea
27	chr7:127609400-127635200	Weak transcription	Fetal Kidney	kidney
28	chr7:127612800-127617800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr7:127612800-127618200	Strong transcription	K562	blood
30	chr7:127613000-127617800	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr7:127613600-127619800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr7:127613800-127623400	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr7:127614000-127631000	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr7:127614200-127617800	Strong transcription	Primary B cells from cord blood	blood
35	chr7:127614400-127618000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr7:127614400-127630600	Weak transcription	Stomach Smooth Muscle	stomach
37	chr7:127614800-127617800	Weak transcription	HSMM	muscle
38	chr7:127615000-127619000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr7:127615400-127619000	Strong transcription	Liver	Liver
40	chr7:127615600-127617800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr7:127615600-127619600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr7:127615800-127617800	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr7:127615800-127625000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr7:127616000-127618200	Strong transcription	Primary T helper cells PMA-I stimulated	--
45	chr7:127616000-127618200	Strong transcription	NHEK	skin
46	chr7:127616000-127618600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr7:127616200-127617800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr7:127616200-127618000	Strong transcription	Primary B cells from peripheral blood	blood
49	chr7:127616200-127619800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
50	chr7:127616200-127623800	Weak transcription	HSMMtube	muscle

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