Variant report

Variant	rs12076607
Chromosome Location	chr1:62459371-62459372
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1112774	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12078747	1.00[ASN][1000 genomes]
rs17122901	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1888984	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1888985	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1888986	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2067506	0.81[AFR][1000 genomes]
rs35393759	0.81[AFR][1000 genomes]
rs56683043	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56945957	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58151949	1.00[EUR][1000 genomes]
rs58402439	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59469474	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60382601	1.00[EUR][1000 genomes]
rs6656983	1.00[EUR][1000 genomes]
rs6693783	1.00[EUR][1000 genomes]
rs6703123	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74076886	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74076890	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74079609	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7516950	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7521447	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7555002	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	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
7	esv2753481	chr1:62424207-62478878	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv546416	chr1:62437872-62492215	Weak transcription Enhancers 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
9	nsv1005178	chr1:62439219-62468653	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv999481	chr1:62439219-62472591	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62385000-62494200	Weak transcription	Aorta	Aorta
2	chr1:62409200-62518600	Weak transcription	Pancreas	Pancrea
3	chr1:62424200-62494200	Weak transcription	Esophagus	oesophagus
4	chr1:62441400-62459800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:62444200-62479200	Weak transcription	Fetal Intestine Small	intestine
6	chr1:62446600-62465200	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr1:62446600-62487600	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr1:62446800-62469400	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr1:62447200-62469400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr1:62447400-62481200	Weak transcription	Lung	lung
11	chr1:62448400-62470400	Weak transcription	Ovary	ovary
12	chr1:62453400-62460200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr1:62453600-62461400	Weak transcription	Psoas Muscle	Psoas
14	chr1:62455200-62460200	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr1:62455200-62463000	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr1:62456000-62459600	Strong transcription	Rectal Mucosa Donor 31	rectum
17	chr1:62456200-62478600	Weak transcription	Stomach Smooth Muscle	stomach
18	chr1:62456800-62459600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:62456800-62459800	Enhancers	NHEK	skin
20	chr1:62457000-62459400	Strong transcription	Liver	Liver
21	chr1:62457000-62460000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr1:62457000-62460000	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr1:62457000-62460000	Strong transcription	Fetal Intestine Large	intestine
24	chr1:62457000-62473400	Weak transcription	Primary T cells from cord blood	blood
25	chr1:62457400-62459800	Weak transcription	Adipose Nuclei	Adipose
26	chr1:62457400-62460000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr1:62458000-62459800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr1:62458000-62460200	Enhancers	HMEC	breast
29	chr1:62458200-62459400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr1:62458200-62459600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr1:62458200-62460200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr1:62458400-62459600	Strong transcription	Sigmoid Colon	Sigmoid Colon
33	chr1:62458400-62460000	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr1:62458400-62461400	Weak transcription	Fetal Brain Female	brain
35	chr1:62458600-62459400	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr1:62458600-62459400	Strong transcription	Left Ventricle	heart
37	chr1:62458600-62459400	Enhancers	NH-A	brain
38	chr1:62458600-62459600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr1:62458600-62460000	Enhancers	Fetal Kidney	kidney
40	chr1:62458800-62459400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr1:62458800-62459600	Enhancers	Placenta Amnion	Placenta Amnion
42	chr1:62458800-62460200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr1:62458800-62521400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr1:62459000-62459400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr1:62459000-62459400	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
46	chr1:62459000-62459600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr1:62459000-62459600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr1:62459000-62459600	Enhancers	Stomach Mucosa	stomach
49	chr1:62459000-62484000	Weak transcription	Duodenum Mucosa	Duodenum
50	chr1:62459000-62516000	Weak transcription	Rectal Mucosa Donor 29	rectum

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