Variant report

Variant	rs7620178
Chromosome Location	chr3:156966258-156966259
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10212545	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10451871	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10451916	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1046938	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10513507	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11926167	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12629549	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12637518	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12696045	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13061214	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13081036	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13081038	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13084070	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13084522	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1392799	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1403103	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1500925	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1587534	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1587535	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1608127	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16827350	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16827384	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2088814	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2133952	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35217153	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3749214	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4383468	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4563363	0.83[AMR][1000 genomes]
rs4632503	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4680342	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4680344	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4680346	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4680348	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6441114	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6441121	0.83[AMR][1000 genomes]
rs6441122	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6441123	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67196056	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6767619	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6773061	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6780831	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6781991	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6783595	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6789178	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6805114	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6808284	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6808457	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6809003	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6809394	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7625059	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7636185	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7638194	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7642179	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7647643	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs924517	0.83[AMR][1000 genomes]
rs9289978	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9289979	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9289980	0.82[AMR][1000 genomes]
rs9811195	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9827676	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9831830	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9838724	0.81[AMR][1000 genomes]
rs9848409	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9849168	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9858423	0.82[EUR][1000 genomes]
rs9861469	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9867618	0.83[AMR][1000 genomes]
rs9872340	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829766	chr3:156811536-157020551	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
2	nsv877687	chr3:156924793-157044184	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156955200-156966600	Weak transcription	Pancreas	Pancrea
2	chr3:156957600-156966600	Weak transcription	Lung	lung
3	chr3:156958400-156971200	Weak transcription	Primary B cells from cord blood	blood
4	chr3:156963400-156966600	Enhancers	Brain Angular Gyrus	brain
5	chr3:156964200-156966600	Enhancers	Brain Substantia Nigra	brain
6	chr3:156964400-156966400	Enhancers	Brain Inferior Temporal Lobe	brain
7	chr3:156964600-156966600	Enhancers	Brain Cingulate Gyrus	brain
8	chr3:156964600-156966600	Enhancers	Brain Hippocampus Middle	brain
9	chr3:156964800-156966600	Enhancers	Colon Smooth Muscle	Colon
10	chr3:156964800-156966600	Enhancers	Skeletal Muscle Male	skeletal muscle
11	chr3:156964800-156966800	Enhancers	Primary hematopoietic stem cells	blood
12	chr3:156964800-156967000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr3:156964800-156967200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr3:156964800-156968600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr3:156965000-156966400	Enhancers	Brain Anterior Caudate	brain
16	chr3:156965000-156966400	Enhancers	NHDF-Ad	bronchial
17	chr3:156965000-156966600	Enhancers	Hela-S3	cervix
18	chr3:156965000-156966600	Enhancers	HUVEC	blood vessel
19	chr3:156965000-156967000	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr3:156965000-156967200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr3:156965000-156967200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr3:156965000-156967600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr3:156965000-156968600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr3:156965200-156966400	Weak transcription	Ovary	ovary
25	chr3:156965200-156966600	Enhancers	Fetal Heart	heart
26	chr3:156965200-156966600	Weak transcription	Fetal Stomach	stomach
27	chr3:156965200-156966600	Enhancers	Rectal Smooth Muscle	rectum
28	chr3:156965200-156966600	Enhancers	HSMMtube	muscle
29	chr3:156965200-156967200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr3:156965200-156967200	Enhancers	HSMM	muscle
31	chr3:156965200-156967200	Enhancers	Osteobl	bone
32	chr3:156965200-156967400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr3:156965200-156968200	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr3:156965200-156968600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:156965400-156966600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr3:156965400-156966600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr3:156965400-156966600	Weak transcription	K562	blood
38	chr3:156965400-156967000	Enhancers	NHLF	lung
39	chr3:156965600-156966800	Weak transcription	Right Atrium	heart
40	chr3:156965600-156968000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr3:156965800-156966600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr3:156965800-156966600	Enhancers	Skeletal Muscle Female	skeletal muscle
43	chr3:156965800-156966800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr3:156965800-156967000	Enhancers	NHEK	skin
45	chr3:156965800-156967200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr3:156965800-156967200	Enhancers	Psoas Muscle	Psoas
47	chr3:156965800-156969200	Enhancers	Left Ventricle	heart
48	chr3:156966000-156966400	Weak transcription	Adipose Nuclei	Adipose
49	chr3:156966000-156967600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr3:156966000-156967600	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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