Variant report

Variant	rs9812169
Chromosome Location	chr3:156528401-156528402
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:156467361..156469859-chr3:156528012..156530054,3	MCF-7	breast:
2	chr3:156527949..156530289-chr3:156543460..156546861,3	K562	blood:
3	chr3:156388866..156397270-chr3:156524172..156537549,71	MCF-7	breast:
4	chr3:156392305..156394108-chr3:156527817..156529889,2	MCF-7	breast:
5	chr3:156527592..156531932-chr3:156540848..156546879,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000240875	Chromatin interaction
ENSG00000163659	Chromatin interaction
ENSG00000197980	Chromatin interaction
ENSG00000243926	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 11 )

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

rs_ID	r²[population]
rs10936037	0.85[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs10936038	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11711674	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11717133	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12492804	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12497539	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13072896	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13086516	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs13097325	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1430410	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1430411	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1560415	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1560416	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1835372	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4680305	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59717073	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6776157	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7641929	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9818684	0.81[AMR][1000 genomes]
rs9820830	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9837271	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9842198	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9858861	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[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	nsv428745	chr3:156405054-156577840	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS 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	49 gene(s)	inside rSNPs	diseases
2	nsv877685	chr3:156444383-156611676	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
3	nsv877686	chr3:156489509-156557697	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
4	nsv967081	chr3:156527290-156529310	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs9812169	LINC00886	cis	Thyroid	GTEx
rs9812169	LINC00886	cis	Nerve Tibial	GTEx
rs9812169	LINC00886	cis	Artery Aorta	GTEx
rs9812169	LINC00886	cis	lung	GTEx
rs9812169	LINC00886	cis	Skin Sun Exposed Lower leg	GTEx
rs9812169	LINC00886	cis	Adipose Subcutaneous	GTEx
rs9812169	LINC00886	cis	Stomach	GTEx
rs9812169	LINC00886	cis	Esophagus Mucosa	GTEx
rs9812169	LINC00886	cis	Muscle Skeletal	GTEx
rs9812169	LINC00886	cis	Esophagus Muscularis	GTEx
rs9812169	LINC00886	cis	Artery Tibial	GTEx

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156502800-156529000	Weak transcription	Liver	Liver
2	chr3:156511200-156529000	Weak transcription	Primary T cells from cord blood	blood
3	chr3:156511400-156530400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr3:156517400-156529000	Weak transcription	A549	lung
5	chr3:156518000-156529800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr3:156520200-156530400	Weak transcription	Right Ventricle	heart
7	chr3:156522200-156530400	Weak transcription	Gastric	stomach
8	chr3:156522400-156529000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr3:156525000-156529000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr3:156526200-156528600	Weak transcription	HSMMtube	muscle
11	chr3:156526200-156529000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr3:156526200-156529000	Weak transcription	K562	blood
13	chr3:156526200-156530600	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr3:156526400-156528600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr3:156526400-156529000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr3:156526400-156529000	Weak transcription	NH-A	brain
17	chr3:156526400-156530600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr3:156526600-156529000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr3:156526800-156528800	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr3:156527000-156529000	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr3:156527000-156529000	Weak transcription	Osteobl	bone
22	chr3:156527000-156529200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr3:156527000-156530400	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr3:156527200-156528800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr3:156527200-156533200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr3:156527400-156531600	Enhancers	Fetal Intestine Small	intestine
27	chr3:156527400-156533800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr3:156527800-156529000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr3:156527800-156533000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr3:156527800-156533800	Enhancers	HMEC	breast
31	chr3:156528200-156528800	Genic enhancers	NHEK	skin
32	chr3:156528200-156530000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr3:156528200-156533600	Weak transcription	Stomach Smooth Muscle	stomach
34	chr3:156528400-156528600	Strong transcription	GM12878-XiMat	blood
35	chr3:156528400-156528800	Enhancers	Esophagus	oesophagus
36	chr3:156528400-156528800	ZNF genes & repeats	Lung	lung
37	chr3:156528400-156529000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr3:156528400-156529400	Enhancers	Duodenum Mucosa	Duodenum
39	chr3:156528400-156530800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr3:156528400-156531000	Enhancers	Rectal Mucosa Donor 31	rectum
41	chr3:156528400-156531200	Enhancers	Fetal Intestine Large	intestine
42	chr3:156528400-156531200	Enhancers	HUVEC	blood vessel
43	chr3:156528400-156531200	Enhancers	NHDF-Ad	bronchial
44	chr3:156528400-156532800	Enhancers	Breast Myoepithelial Primary Cells	Breast

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