Variant report

Variant	rs28470208
Chromosome Location	chr7:65584700-65584701
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:65579988..65582211-chr7:65582533..65585744,4	MCF-7	breast:
2	chr7:65578365..65582284-chr7:65582321..65585253,7	MCF-7	breast:
3	chr7:65568916..65570554-chr7:65582641..65585238,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GUSB-3	chr7:65584590-65584729	ENSG00000234185.1
2	lnc-GUSB-3	chr7:65584590-65584729	ENSG00000234185.2

Variant related genes	Relation type
ENSG00000241258	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10240249	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10253922	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10256544	0.84[AMR][1000 genomes]
rs10268656	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10271553	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1129531	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1167390	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1167399	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1167406	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1167408	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1167612	0.83[AMR][1000 genomes]
rs11971949	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs11974264	0.83[AFR][1000 genomes]
rs13240492	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs13242721	0.85[AFR][1000 genomes]
rs13245728	0.99[AFR][1000 genomes]
rs13309935	0.88[AMR][1000 genomes]
rs1540651	0.82[AFR][1000 genomes]
rs1612452	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1616988	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1976200	0.99[AFR][1000 genomes]
rs1983372	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2087647	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2249458	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2420168	0.83[AMR][1000 genomes]
rs2420173	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2420174	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2460430	0.93[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2460432	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs28391294	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2949696	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs34550048	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35034167	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4368860	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4612218	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4718319	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55962648	0.85[AMR][1000 genomes]
rs57866200	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59466412	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62467451	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6946143	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6951787	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6957690	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6958484	0.85[AMR][1000 genomes]
rs6961717	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6967708	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs709608	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs709609	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7782806	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7786892	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7801282	0.85[AMR][1000 genomes]
rs7809814	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs780998	0.81[AMR][1000 genomes]
rs875971	0.85[AMR][1000 genomes]
rs880166	0.85[AMR][1000 genomes]
rs908915	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9767916	0.93[AMR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2761079	chr7:65092426-65689733	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv532124	chr7:65371521-66234730	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	125 gene(s)	inside rSNPs	diseases
3	nsv1021186	chr7:65492601-65663438	Active TSS Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs28470208	ASL	Cis_1M	lymphoblastoid	RTeQTL
rs28470208	GS1-124K5.2	cis	Whole Blood	GTEx
rs28470208	RP4-756H11.3	cis	Esophagus Muscularis	GTEx
rs28470208	RP4-756H11.3	cis	Heart Left Ventricle	GTEx
rs28470208	RP4-756H11.3	cis	Adipose Subcutaneous	GTEx
rs28470208	GS1-124K5.4	cis	Skin Sun Exposed Lower leg	GTEx
rs28470208	GTF2IRD1P1	cis	Thyroid	GTEx
rs28470208	GS1-124K5.11	cis	Thyroid	GTEx
rs28470208	RP4-756H11.3	cis	lung	GTEx
rs28470208	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs28470208	RNU6-96P	cis	Thyroid	GTEx
rs28470208	RP4-756H11.3	cis	Nerve Tibial	GTEx
rs28470208	RP4-756H11.3	cis	Muscle Skeletal	GTEx
rs28470208	RP4-756H11.3	cis	Artery Tibial	GTEx
rs28470208	LINC00174	cis	Thyroid	GTEx
rs28470208	GS1-124K5.4	cis	Stomach	GTEx
rs28470208	RP4-756H11.3	cis	Thyroid	GTEx
rs28470208	RP4-756H11.3	cis	Esophagus Mucosa	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65580600-65591000	Weak transcription	Ovary	ovary
2	chr7:65580600-65600600	Weak transcription	Aorta	Aorta
3	chr7:65580800-65606800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr7:65581000-65587400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr7:65581000-65589600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr7:65581000-65595600	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr7:65581000-65595600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr7:65581000-65595800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr7:65581000-65597000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr7:65581000-65617200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr7:65581200-65584800	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr7:65581200-65586200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr7:65581200-65590200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr7:65581200-65590600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr7:65581200-65596000	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr7:65581400-65589600	Weak transcription	Rectal Smooth Muscle	rectum
17	chr7:65581400-65590400	Weak transcription	Osteobl	bone
18	chr7:65581400-65595400	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr7:65581400-65595800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr7:65581400-65596400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr7:65581600-65584800	Genic enhancers	Dnd41	blood
22	chr7:65581600-65589400	Weak transcription	HSMMtube	muscle
23	chr7:65581600-65604800	Weak transcription	Colonic Mucosa	Colon
24	chr7:65581800-65584800	Genic enhancers	K562	blood
25	chr7:65581800-65589400	Weak transcription	HSMM	muscle
26	chr7:65581800-65589600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr7:65581800-65590200	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr7:65581800-65595200	Weak transcription	Fetal Muscle Leg	muscle
29	chr7:65581800-65595600	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr7:65581800-65595800	Weak transcription	Stomach Smooth Muscle	stomach
31	chr7:65582000-65584800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr7:65582000-65595200	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr7:65582000-65595800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr7:65582200-65584800	Enhancers	Liver	Liver
35	chr7:65582400-65584800	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr7:65582400-65589600	Weak transcription	NHDF-Ad	bronchial
37	chr7:65582400-65608200	Weak transcription	Fetal Brain Male	brain
38	chr7:65582600-65584800	Strong transcription	Fetal Stomach	stomach
39	chr7:65582600-65586400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr7:65582600-65595000	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr7:65582600-65596400	Weak transcription	NH-A	brain
42	chr7:65582800-65585000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr7:65582800-65586000	Enhancers	Adipose Nuclei	Adipose
44	chr7:65583000-65585600	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr7:65583000-65586800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr7:65583000-65586800	Weak transcription	Hela-S3	cervix
47	chr7:65583000-65589600	Weak transcription	Small Intestine	intestine
48	chr7:65583000-65594400	Weak transcription	Duodenum Mucosa	Duodenum
49	chr7:65583000-65596000	Weak transcription	Thymus	Thymus
50	chr7:65583200-65584800	Strong transcription	Primary B cells from peripheral blood	blood

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