Variant report

Variant	rs56095564
Chromosome Location	chr2:153254184-153254185
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs13386403	0.88[EUR][1000 genomes]
rs13391023	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13396439	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13397890	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13402243	0.88[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs13405110	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13405341	0.80[ASN][1000 genomes]
rs13405868	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13414887	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13418521	0.80[ASN][1000 genomes]
rs13418748	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13419000	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13419948	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13428569	0.91[EUR][1000 genomes]
rs13430448	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16831028	0.82[AFR][1000 genomes]
rs2345873	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3811577	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3890370	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61292193	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62180766	0.93[ASN][1000 genomes]
rs6761815	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73967855	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73967856	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73967858	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73967990	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7593505	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834419	chr2:153179420-153381476	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv1005012	chr2:153206764-153273886	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	esv3693436	chr2:153219836-153479857	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv875291	chr2:153251742-153339823	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:153233800-153255400	Weak transcription	NHEK	skin
2	chr2:153237400-153255400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr2:153237400-153255400	Weak transcription	HMEC	breast
4	chr2:153238600-153258600	Weak transcription	Left Ventricle	heart
5	chr2:153241200-153255400	Weak transcription	Pancreas	Pancrea
6	chr2:153246600-153266600	Enhancers	Brain Substantia Nigra	brain
7	chr2:153247000-153257800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr2:153247200-153255400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr2:153247400-153255400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr2:153247400-153277600	Weak transcription	Fetal Intestine Small	intestine
11	chr2:153247800-153258800	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr2:153249200-153254200	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr2:153249600-153255400	Weak transcription	Gastric	stomach
14	chr2:153249600-153255400	Weak transcription	Lung	lung
15	chr2:153249600-153259000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr2:153250000-153254200	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr2:153250400-153257600	Weak transcription	HepG2	liver
18	chr2:153250800-153258800	Weak transcription	Small Intestine	intestine
19	chr2:153252000-153255400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr2:153252000-153269800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr2:153252400-153258000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr2:153252800-153255600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr2:153253000-153257200	Weak transcription	Stomach Smooth Muscle	stomach
24	chr2:153253000-153257600	Enhancers	Brain Inferior Temporal Lobe	brain
25	chr2:153253000-153258400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
26	chr2:153253000-153258800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr2:153253000-153260600	Enhancers	Brain Anterior Caudate	brain
28	chr2:153253200-153254600	Weak transcription	Ovary	ovary
29	chr2:153253200-153255200	Weak transcription	A549	lung
30	chr2:153253200-153257800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr2:153253200-153258000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr2:153253200-153258600	Weak transcription	Fetal Muscle Leg	muscle
33	chr2:153253200-153258800	Weak transcription	Right Atrium	heart
34	chr2:153253200-153259000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr2:153253200-153259600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr2:153253200-153260000	Weak transcription	Aorta	Aorta
37	chr2:153253200-153261600	Weak transcription	HSMM	muscle
38	chr2:153253200-153261600	Weak transcription	NH-A	brain
39	chr2:153253200-153261600	Weak transcription	NHLF	lung
40	chr2:153253200-153261800	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr2:153253200-153262800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr2:153253200-153263200	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr2:153253200-153263400	Enhancers	Brain Hippocampus Middle	brain
44	chr2:153253200-153263800	Weak transcription	Fetal Brain Female	brain
45	chr2:153253200-153266400	Enhancers	Brain Cingulate Gyrus	brain
46	chr2:153253400-153259000	Weak transcription	Adipose Nuclei	Adipose
47	chr2:153253600-153254200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr2:153253600-153255000	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr2:153253600-153255200	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr2:153253600-153257800	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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