Variant report

Variant	rs12142556
Chromosome Location	chr1:92777728-92777729
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs58142139	0.88[AFR][1000 genomes]
rs58176898	0.82[AFR][1000 genomes]
rs58820626	0.88[AFR][1000 genomes]
rs6671543	0.94[AFR][1000 genomes]
rs6679259	0.81[AFR][1000 genomes]
rs6694248	0.85[AFR][1000 genomes]
rs6695475	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs72958746	0.86[AFR][1000 genomes]
rs72958774	0.95[AFR][1000 genomes]
rs72958796	0.99[AFR][1000 genomes]
rs72960815	0.99[AFR][1000 genomes]
rs72960831	0.94[AFR][1000 genomes]
rs72960835	0.94[AFR][1000 genomes]
rs72960860	0.93[AFR][1000 genomes]
rs72960870	0.88[AFR][1000 genomes]
rs7513631	0.89[AFR][1000 genomes]
rs7519603	1.00[YRI][hapmap]

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	nsv1012864	chr1:92067100-92827761	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv535029	chr1:92067100-92827761	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv530438	chr1:92091957-92827760	Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv530046	chr1:92277460-92799794	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv871508	chr1:92478130-92781579	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	nsv830592	chr1:92669282-92805629	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv870667	chr1:92697188-92813741	Active TSS Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
8	nsv871352	chr1:92761127-92807238	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
9	nsv870854	chr1:92765102-92807238	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
10	nsv871387	chr1:92765102-92813741	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:92765200-92791600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:92765200-92792000	Weak transcription	Aorta	Aorta
3	chr1:92765200-92792000	Weak transcription	Esophagus	oesophagus
4	chr1:92765600-92778400	Weak transcription	Fetal Stomach	stomach
5	chr1:92765600-92789600	Weak transcription	Psoas Muscle	Psoas
6	chr1:92765600-92791000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr1:92765600-92791600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr1:92765600-92791800	Weak transcription	Lung	lung
9	chr1:92765600-92791800	Weak transcription	Pancreas	Pancrea
10	chr1:92765600-92791800	Weak transcription	Right Ventricle	heart
11	chr1:92765600-92792000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:92765600-92792000	Weak transcription	Spleen	Spleen
13	chr1:92765800-92786200	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr1:92765800-92789000	Weak transcription	Ovary	ovary
15	chr1:92765800-92789200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr1:92765800-92791600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr1:92765800-92791800	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr1:92765800-92791800	Weak transcription	Gastric	stomach
19	chr1:92765800-92850000	Weak transcription	Small Intestine	intestine
20	chr1:92766000-92792000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr1:92766200-92789000	Weak transcription	Brain Cingulate Gyrus	brain
22	chr1:92766400-92791600	Weak transcription	Brain Hippocampus Middle	brain
23	chr1:92767200-92779800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr1:92767200-92783600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:92767400-92783200	Weak transcription	Fetal Heart	heart
26	chr1:92768800-92779600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr1:92770600-92789000	Weak transcription	Rectal Smooth Muscle	rectum
28	chr1:92770800-92783000	Weak transcription	HUVEC	blood vessel
29	chr1:92770800-92788800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr1:92771000-92791400	Weak transcription	NHEK	skin
31	chr1:92771600-92782600	Weak transcription	K562	blood
32	chr1:92771800-92781800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr1:92771800-92789000	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr1:92771800-92789000	Weak transcription	A549	lung
35	chr1:92771800-92794800	Weak transcription	Brain Angular Gyrus	brain
36	chr1:92771800-92823800	Weak transcription	Colonic Mucosa	Colon
37	chr1:92772000-92789000	Weak transcription	HepG2	liver
38	chr1:92772000-92789400	Weak transcription	Fetal Brain Male	brain
39	chr1:92772600-92781400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr1:92773000-92800800	Weak transcription	NHDF-Ad	bronchial
41	chr1:92773200-92781000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr1:92773600-92786200	Weak transcription	Brain Germinal Matrix	brain
43	chr1:92773800-92785800	Weak transcription	Liver	Liver
44	chr1:92773800-92791800	Weak transcription	NHLF	lung
45	chr1:92774000-92786200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr1:92774000-92791800	Weak transcription	Brain Anterior Caudate	brain
47	chr1:92774200-92777800	Weak transcription	Primary hematopoietic stem cells	blood
48	chr1:92774200-92778800	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr1:92774200-92779400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr1:92774200-92780800	Weak transcription	HUES6 Cell Line	embryonic stem cell

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