Variant report

Variant	rs2039620
Chromosome Location	chr1:225682175-225682176
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10799320	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10915831	0.83[ASN][1000 genomes]
rs10915836	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12032961	0.87[AFR][1000 genomes]
rs12034829	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1340865	0.81[ASN][1000 genomes]
rs1891000	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2185528	0.83[ASN][1000 genomes]
rs3856157	0.82[ASN][1000 genomes]
rs3893032	0.82[ASN][1000 genomes]
rs4233220	0.87[ASN][1000 genomes]
rs4554690	0.93[ASN][1000 genomes]
rs499782	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6426075	0.82[ASN][1000 genomes]
rs6692054	0.87[ASN][1000 genomes]
rs6702641	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7522622	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7527014	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7527184	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7529690	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7552953	0.82[ASN][1000 genomes]
rs9426126	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9725758	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832714	chr1:225592333-225805396	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv1004851	chr1:225614140-225684184	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv873227	chr1:225656388-225687981	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv8880	chr1:225656408-225687710	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv826842	chr1:225658062-225686586	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv441740	chr1:225659217-225684196	Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
7	nsv433350	chr1:225665284-225686025	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS	Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
8	nsv873228	chr1:225665284-225687981	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
9	esv2756886	chr1:225665694-225703485	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
10	esv2759003	chr1:225665694-225703485	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
11	nsv873229	chr1:225668031-225685928	Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
12	nsv873230	chr1:225668524-225687981	Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS	Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
13	nsv4720	chr1:225673218-225718009	Genic enhancers Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225663200-225683800	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr1:225663200-225686400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:225663200-225696400	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr1:225663400-225686000	Weak transcription	A549	lung
5	chr1:225666000-225696800	Weak transcription	Esophagus	oesophagus
6	chr1:225667400-225684400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:225669000-225687800	Weak transcription	Placenta	Placenta
8	chr1:225669800-225696800	Weak transcription	Pancreas	Pancrea
9	chr1:225670600-225684200	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr1:225670800-225682200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr1:225670800-225683800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr1:225670800-225683800	Weak transcription	HSMMtube	muscle
13	chr1:225670800-225686400	Weak transcription	Ovary	ovary
14	chr1:225670800-225688400	Weak transcription	Duodenum Mucosa	Duodenum
15	chr1:225671600-225683800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr1:225671600-225685000	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr1:225672000-225683600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr1:225672200-225685200	Weak transcription	NHDF-Ad	bronchial
19	chr1:225672200-225696800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr1:225672200-225696800	Weak transcription	Brain Germinal Matrix	brain
21	chr1:225672400-225683800	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr1:225672600-225683000	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr1:225672800-225693800	Weak transcription	Left Ventricle	heart
24	chr1:225673200-225683600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr1:225673400-225684000	Weak transcription	Fetal Muscle Trunk	muscle
26	chr1:225673600-225693800	Weak transcription	Fetal Muscle Leg	muscle
27	chr1:225673800-225686400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr1:225674400-225696800	Weak transcription	Aorta	Aorta
29	chr1:225674800-225683800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr1:225674800-225693800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr1:225675200-225687400	Weak transcription	Stomach Mucosa	stomach
32	chr1:225676200-225696400	Weak transcription	Gastric	stomach
33	chr1:225677000-225686600	Weak transcription	Fetal Stomach	stomach
34	chr1:225677200-225682200	Weak transcription	Fetal Lung	lung
35	chr1:225677200-225685000	Weak transcription	Fetal Brain Male	brain
36	chr1:225677200-225686400	Weak transcription	Brain Hippocampus Middle	brain
37	chr1:225677200-225688400	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr1:225677200-225688400	Weak transcription	Brain Anterior Caudate	brain
39	chr1:225677200-225696000	Weak transcription	Rectal Smooth Muscle	rectum
40	chr1:225677200-225696400	Weak transcription	Brain Angular Gyrus	brain
41	chr1:225677200-225696400	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr1:225677200-225696400	Weak transcription	Brain Substantia Nigra	brain
43	chr1:225677200-225696400	Weak transcription	Colon Smooth Muscle	Colon
44	chr1:225677200-225696600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr1:225677200-225696600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr1:225677200-225696600	Weak transcription	Psoas Muscle	Psoas
47	chr1:225677200-225703600	Weak transcription	Fetal Brain Female	brain
48	chr1:225677400-225686000	Weak transcription	Stomach Smooth Muscle	stomach
49	chr1:225677400-225686200	Weak transcription	NHLF	lung
50	chr1:225677800-225683600	Weak transcription	Fetal Intestine Large	intestine

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