Variant report

Variant	rs10889275
Chromosome Location	chr1:62408501-62408502
allele	A/G
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	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10889274	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10889276	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11207867	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs11207871	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11207873	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11207875	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11485616	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11801545	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11802946	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11804624	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11807297	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11809363	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11811508	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12064034	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12064276	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12069154	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12069359	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12070855	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12074521	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12085283	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12097605	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12097637	0.83[AMR][1000 genomes]
rs12239276	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61743112	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs74076821	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs74076835	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9970060	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9970292	0.97[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:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62336000-62408600	Weak transcription	Pancreas	Pancrea
2	chr1:62346200-62417600	Weak transcription	Rectal Smooth Muscle	rectum
3	chr1:62350600-62428200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr1:62350800-62417600	Weak transcription	Ovary	ovary
5	chr1:62353800-62408800	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr1:62361600-62408800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:62362000-62408600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr1:62372400-62408800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr1:62372400-62417600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr1:62374600-62410600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr1:62376200-62417600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:62380600-62408600	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr1:62380800-62410000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr1:62381000-62416000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr1:62381200-62417400	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr1:62381200-62418400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr1:62384600-62408800	Weak transcription	Fetal Intestine Large	intestine
18	chr1:62385000-62494200	Weak transcription	Aorta	Aorta
19	chr1:62385400-62408600	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr1:62386000-62408600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr1:62391800-62409000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr1:62392000-62408800	Weak transcription	Gastric	stomach
23	chr1:62392600-62408600	Weak transcription	Stomach Mucosa	stomach
24	chr1:62392600-62408800	Weak transcription	Left Ventricle	heart
25	chr1:62393800-62422400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr1:62395000-62408600	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr1:62395000-62410800	Weak transcription	Liver	Liver
28	chr1:62396200-62408600	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr1:62396200-62416000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr1:62396200-62417200	Weak transcription	HMEC	breast
31	chr1:62396400-62408600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr1:62396400-62418000	Weak transcription	Fetal Kidney	kidney
33	chr1:62397600-62408600	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr1:62398200-62408600	Weak transcription	Esophagus	oesophagus
35	chr1:62398800-62408600	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr1:62400600-62417600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr1:62401400-62408800	Weak transcription	Lung	lung
38	chr1:62406000-62408800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr1:62406600-62430200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr1:62407000-62409600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr1:62407200-62417400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr1:62408000-62409200	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr1:62408000-62409200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr1:62408200-62408600	Strong transcription	Fetal Intestine Small	intestine
45	chr1:62408200-62408600	Weak transcription	Fetal Stomach	stomach
46	chr1:62408200-62408600	Strong transcription	NHEK	skin
47	chr1:62408200-62408800	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr1:62408200-62408800	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
49	chr1:62408200-62409200	Strong transcription	Duodenum Mucosa	Duodenum
50	chr1:62408200-62409400	Strong transcription	Sigmoid Colon	Sigmoid Colon

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