Variant report

Variant	rs73164088
Chromosome Location	chr3:157874533-157874534
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:157867634..157869711-chr3:157873897..157875797,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SHOX2-3	chr3:157873661-157876196	refGeneNc_1685_NR_027954

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12486445	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12495621	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2362247	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4542974	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55638807	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73164073	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73164083	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73164089	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73164094	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73166303	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73166305	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73166307	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73166311	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73166326	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73166328	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013391	chr3:157505943-158115553	Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv536775	chr3:157505943-158115553	Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1002378	chr3:157715428-158673414	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv829768	chr3:157832878-158012070	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv877689	chr3:157858930-158133307	Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:157837600-157877600	Weak transcription	Fetal Heart	heart
2	chr3:157843600-157886800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr3:157846200-157875200	Weak transcription	Gastric	stomach
4	chr3:157846200-157893400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr3:157846200-157893600	Weak transcription	Aorta	Aorta
6	chr3:157846600-157878600	Weak transcription	HSMM	muscle
7	chr3:157846800-157874600	Weak transcription	Fetal Lung	lung
8	chr3:157846800-157876800	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr3:157846800-157876800	Weak transcription	K562	blood
10	chr3:157846800-157894400	Weak transcription	Brain Hippocampus Middle	brain
11	chr3:157847200-157876800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr3:157848000-157888200	Weak transcription	Thymus	Thymus
13	chr3:157848200-157876200	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr3:157848200-157886800	Weak transcription	Ovary	ovary
15	chr3:157849400-157894400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr3:157850600-157886400	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr3:157854600-157911800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr3:157856200-157877000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr3:157856200-157894400	Weak transcription	Primary B cells from peripheral blood	blood
20	chr3:157856400-157877000	Weak transcription	A549	lung
21	chr3:157856400-157878600	Weak transcription	Hela-S3	cervix
22	chr3:157856400-157879600	Weak transcription	Adipose Nuclei	Adipose
23	chr3:157856400-157885400	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr3:157856400-157892400	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr3:157860800-157886800	Weak transcription	Left Ventricle	heart
26	chr3:157866400-157877000	Weak transcription	Stomach Mucosa	stomach
27	chr3:157866400-157885200	Weak transcription	GM12878-XiMat	blood
28	chr3:157867400-157885400	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr3:157868200-157916200	Weak transcription	Primary B cells from cord blood	blood
30	chr3:157869400-157887600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr3:157870000-157878600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr3:157870000-157879000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr3:157870200-157876800	Weak transcription	NHDF-Ad	bronchial
34	chr3:157870200-157878400	Weak transcription	HMEC	breast
35	chr3:157870200-157878600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr3:157870600-157878600	Weak transcription	NHEK	skin
37	chr3:157870800-157876800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr3:157871000-157877000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr3:157871000-157877000	Weak transcription	Osteobl	bone
40	chr3:157871000-157878800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr3:157873200-157902000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr3:157873400-157876600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr3:157873800-157875400	Strong transcription	Primary hematopoietic stem cells	blood
44	chr3:157873800-157879000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr3:157874000-157877200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr3:157874000-157884200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr3:157874000-157885600	Weak transcription	Primary T cells from cord blood	blood
48	chr3:157874000-157889600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr3:157874400-157875400	Strong transcription	Dnd41	blood

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