Variant report

Variant	rs709608
Chromosome Location	chr7:65559180-65559181
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:65558787..65560603-chr7:65563146..65565504,2	K562	blood:
2	chr7:65553071..65556091-chr7:65557969..65560559,3	K562	blood:
3	chr7:65553870..65556493-chr7:65557969..65560001,3	K562	blood:
4	chr7:65539544..65541876-chr7:65558237..65561836,3	K562	blood:

Variant related genes	Relation type
ENSG00000126522	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10240249	0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10253922	0.81[AMR][1000 genomes]
rs10268656	0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10271553	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1129531	0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1167390	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1167399	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1167406	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1167408	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1182882	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11971949	0.82[AMR][1000 genomes]
rs13240492	0.81[AMR][1000 genomes]
rs13245728	0.80[AFR][1000 genomes]
rs13247295	0.80[AMR][1000 genomes]
rs13309935	0.83[AMR][1000 genomes]
rs1612452	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1616988	0.91[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1976200	0.80[AFR][1000 genomes]
rs1983372	0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2087647	0.81[AMR][1000 genomes]
rs2220626	0.82[AMR][1000 genomes]
rs2249458	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2420173	0.86[AMR][1000 genomes]
rs2420174	0.86[AMR][1000 genomes]
rs2460430	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2460432	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28391294	0.81[AMR][1000 genomes]
rs28470208	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs34550048	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs35034167	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4368860	0.93[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4612218	0.88[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4718319	0.84[AMR][1000 genomes]
rs55962648	0.81[AMR][1000 genomes]
rs57866200	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs59466412	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs62467451	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6946143	0.81[AMR][1000 genomes]
rs6951787	0.82[AMR][1000 genomes]
rs6957690	0.82[AMR][1000 genomes]
rs6958484	0.81[AMR][1000 genomes]
rs6961717	0.82[AMR][1000 genomes]
rs6967708	0.84[AMR][1000 genomes]
rs697969	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs697970	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs709609	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7782806	0.84[AMR][1000 genomes]
rs7786892	0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7801282	0.81[AMR][1000 genomes]
rs7809814	0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs780998	0.83[AMR][1000 genomes]
rs875971	0.81[AMR][1000 genomes]
rs880166	0.81[AMR][1000 genomes]
rs908915	0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9767916	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[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	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	nsv888325	chr7:65474919-65575893	Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	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
rs709608	ASL	Cis_1M	lymphoblastoid	RTeQTL
rs709608	RP4-756H11.3	cis	Esophagus Mucosa	GTEx
rs709608	GS1-124K5.2	cis	Whole Blood	GTEx
rs709608	RP4-756H11.3	cis	Thyroid	GTEx
rs709608	RP4-756H11.3	cis	Artery Tibial	GTEx
rs709608	GS1-124K5.11	cis	Thyroid	GTEx
rs709608	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs709608	GTF2IRD1P1	cis	Thyroid	GTEx
rs709608	RP4-756H11.3	cis	Muscle Skeletal	GTEx
rs709608	RP4-756H11.3	cis	Heart Left Ventricle	GTEx
rs709608	RP4-756H11.3	cis	Adipose Subcutaneous	GTEx
rs709608	GS1-124K5.4	cis	Skin Sun Exposed Lower leg	GTEx
rs709608	RNU6-96P	cis	Thyroid	GTEx
rs709608	LINC00174	cis	Thyroid	GTEx
rs709608	RP4-756H11.3	cis	Esophagus Muscularis	GTEx
rs709608	GS1-124K5.4	cis	Stomach	GTEx
rs709608	RP4-756H11.3	cis	lung	GTEx
rs709608	RP4-756H11.3	cis	Nerve Tibial	GTEx

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65541600-65565000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr7:65541800-65564600	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr7:65541800-65564600	Weak transcription	Fetal Brain Female	brain
4	chr7:65541800-65564800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr7:65542000-65559600	Weak transcription	Psoas Muscle	Psoas
6	chr7:65542000-65564600	Weak transcription	Primary B cells from cord blood	blood
7	chr7:65542000-65564800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr7:65542000-65564800	Weak transcription	Aorta	Aorta
9	chr7:65542000-65564800	Weak transcription	HSMM	muscle
10	chr7:65542200-65564600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr7:65542200-65564600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr7:65542200-65564600	Weak transcription	Brain Angular Gyrus	brain
13	chr7:65542200-65564600	Weak transcription	Fetal Kidney	kidney
14	chr7:65542200-65564600	Weak transcription	NH-A	brain
15	chr7:65542200-65564800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr7:65542400-65564400	Weak transcription	Hela-S3	cervix
17	chr7:65542800-65560600	Strong transcription	Fetal Stomach	stomach
18	chr7:65543000-65564600	Weak transcription	NHDF-Ad	bronchial
19	chr7:65543200-65564400	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr7:65543400-65559200	Strong transcription	Fetal Intestine Large	intestine
21	chr7:65543600-65561400	Strong transcription	Fetal Intestine Small	intestine
22	chr7:65546200-65560600	Strong transcription	Liver	Liver
23	chr7:65548000-65564600	Weak transcription	GM12878-XiMat	blood
24	chr7:65548200-65564600	Weak transcription	Brain Substantia Nigra	brain
25	chr7:65548200-65564800	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr7:65549000-65564600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr7:65549200-65564600	Weak transcription	K562	blood
28	chr7:65549200-65564600	Weak transcription	NHEK	skin
29	chr7:65549400-65564600	Weak transcription	Primary B cells from peripheral blood	blood
30	chr7:65550200-65564400	Weak transcription	Right Atrium	heart
31	chr7:65550600-65564600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr7:65551600-65564800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr7:65551600-65564800	Weak transcription	Primary T cells from cord blood	blood
34	chr7:65551600-65564800	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr7:65552000-65564400	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr7:65552000-65564600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr7:65552000-65564600	Weak transcription	Fetal Lung	lung
38	chr7:65552200-65564400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr7:65552200-65564600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr7:65552200-65564600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr7:65552200-65564600	Weak transcription	Brain Anterior Caudate	brain
42	chr7:65552200-65564600	Weak transcription	A549	lung
43	chr7:65552200-65564600	Weak transcription	HMEC	breast
44	chr7:65552200-65564800	Weak transcription	Left Ventricle	heart
45	chr7:65552400-65564600	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr7:65552400-65564600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr7:65552400-65564600	Weak transcription	Brain Cingulate Gyrus	brain
48	chr7:65552600-65559200	Weak transcription	Fetal Muscle Trunk	muscle
49	chr7:65552600-65563800	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr7:65552600-65564400	Weak transcription	Rectal Smooth Muscle	rectum

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