Variant report

Variant	rs12085283
Chromosome Location	chr1:62412677-62412678
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10047078	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10889274	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10889275	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10889276	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11207867	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs11207871	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11207873	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11207875	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11485616	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11801545	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11802946	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11804624	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11807297	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11809363	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11811508	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12064034	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12064276	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12069154	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12069359	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12070855	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12074521	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12097605	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12097637	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12239276	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61743112	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs74076821	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs74076835	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9970060	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9970292	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv518627	chr1:62279594-62517947	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv522020	chr1:62279594-62517947	Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv531876	chr1:62302313-62504349	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv1004446	chr1:62394631-62813533	Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
5	nsv534984	chr1:62394631-62813533	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
6	nsv1110	chr1:62395723-62454435	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv546415	chr1:62405873-62437872	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv1001667	chr1:62407786-62649838	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62346200-62417600	Weak transcription	Rectal Smooth Muscle	rectum
2	chr1:62350600-62428200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr1:62350800-62417600	Weak transcription	Ovary	ovary
4	chr1:62372400-62417600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr1:62376200-62417600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:62381000-62416000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr1:62381200-62417400	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr1:62381200-62418400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr1:62385000-62494200	Weak transcription	Aorta	Aorta
10	chr1:62393800-62422400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr1:62396200-62416000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr1:62396200-62417200	Weak transcription	HMEC	breast
13	chr1:62396400-62418000	Weak transcription	Fetal Kidney	kidney
14	chr1:62400600-62417600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr1:62406600-62430200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr1:62407200-62417400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:62408800-62416000	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr1:62409000-62413400	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr1:62409000-62416000	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr1:62409000-62436800	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr1:62409200-62416000	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr1:62409200-62416000	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr1:62409200-62416200	Weak transcription	NHEK	skin
24	chr1:62409200-62416600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr1:62409200-62456000	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr1:62409200-62456800	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr1:62409200-62457000	Weak transcription	Fetal Intestine Large	intestine
28	chr1:62409200-62518600	Weak transcription	Pancreas	Pancrea
29	chr1:62409400-62416800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr1:62409400-62417200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr1:62409400-62418000	Weak transcription	Left Ventricle	heart
32	chr1:62409400-62429600	Weak transcription	Gastric	stomach
33	chr1:62409400-62458400	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr1:62409600-62417200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr1:62409800-62416600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr1:62410200-62425200	Weak transcription	Fetal Intestine Small	intestine

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