Variant report

Variant	rs2659914
Chromosome Location	chr7:66156914-66156915
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:66150663..66153524-chr7:66155047..66157975,3	K562	blood:
2	chr7:66151342..66153524-chr7:66155047..66159440,3	K562	blood:
3	chr7:66155376..66157411-chr7:66204000..66206199,2	K562	blood:

Variant related genes	Relation type
ENSG00000272831	Chromatin interaction
ENSG00000154710	Chromatin interaction
ENSG00000243335	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1016265	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10233806	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10244498	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10274883	0.83[AMR][1000 genomes]
rs10950049	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13242290	0.83[AMR][1000 genomes]
rs13308803	0.85[AFR][1000 genomes]
rs1544549	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1962050	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2003300	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2013908	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2109297	0.83[AMR][1000 genomes]
rs2420820	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2659890	0.81[AFR][1000 genomes]
rs2659891	0.83[AFR][1000 genomes]
rs2659892	0.85[AFR][1000 genomes]
rs2659893	0.85[AFR][1000 genomes]
rs2659894	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2659895	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2659897	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2659898	0.85[AFR][1000 genomes]
rs2659900	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2659901	0.82[AFR][1000 genomes]
rs2659904	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2659907	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2659908	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2707824	0.85[AFR][1000 genomes]
rs2707837	0.82[AFR][1000 genomes]
rs2707839	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2707847	0.85[AFR][1000 genomes]
rs3846973	0.83[AMR][1000 genomes]
rs3857687	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4610622	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4718383	0.82[AMR][1000 genomes]
rs58347342	0.82[AFR][1000 genomes]
rs6951302	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6958200	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6969679	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6978178	0.83[AMR][1000 genomes]
rs721717	0.80[AMR][1000 genomes]
rs7782587	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7792762	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs881285	0.83[AMR][1000 genomes]
rs974239	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9791712	0.82[AMR][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	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
2	nsv1026559	chr7:65617368-66370805	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
3	esv3385090	chr7:66146376-66205022	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	esv3401338	chr7:66147493-66206298	Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	nsv970870	chr7:66147890-66158166	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs2659914	GS1-124K5.11	cis	Thyroid	GTEx
rs2659914	GS1-124K5.4	cis	Stomach	GTEx
rs2659914	RNU6-96P	cis	Thyroid	GTEx
rs2659914	RP4-756H11.3	cis	Artery Tibial	GTEx
rs2659914	RP4-756H11.3	cis	Thyroid	GTEx
rs2659914	RP4-756H11.3	cis	Adipose Subcutaneous	GTEx
rs2659914	GTF2IRD1P1	cis	Thyroid	GTEx
rs2659914	RP4-756H11.3	cis	Nerve Tibial	GTEx
rs2659914	ASL	Cis_1M	lymphoblastoid	RTeQTL
rs2659914	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs2659914	RP4-756H11.3	cis	Artery Aorta	GTEx
rs2659914	RP4-756H11.3	cis	lung	GTEx
rs2659914	RP4-756H11.3	cis	Heart Left Ventricle	GTEx
rs2659914	GS1-124K5.4	cis	Artery Aorta	GTEx
rs2659914	RP4-756H11.3	cis	Muscle Skeletal	GTEx
rs2659914	RP4-756H11.3	cis	Esophagus Muscularis	GTEx
rs2659914	RP4-756H11.3	cis	Esophagus Mucosa	GTEx

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66148000-66157200	Weak transcription	Spleen	Spleen
2	chr7:66148000-66157400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr7:66148000-66161800	Weak transcription	Left Ventricle	heart
4	chr7:66148000-66161800	Weak transcription	Right Atrium	heart
5	chr7:66148000-66165600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr7:66148000-66177600	Weak transcription	Aorta	Aorta
7	chr7:66148200-66157800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr7:66148200-66157800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr7:66148200-66157800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr7:66148200-66158400	Weak transcription	Primary T cells from cord blood	blood
11	chr7:66148200-66161800	Weak transcription	Psoas Muscle	Psoas
12	chr7:66148200-66162000	Weak transcription	Gastric	stomach
13	chr7:66148200-66162000	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr7:66148200-66175600	Weak transcription	Primary B cells from cord blood	blood
15	chr7:66148400-66157200	Weak transcription	Fetal Intestine Small	intestine
16	chr7:66148400-66157400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr7:66148400-66157400	Weak transcription	Esophagus	oesophagus
18	chr7:66148400-66157400	Weak transcription	Fetal Muscle Trunk	muscle
19	chr7:66148400-66157800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr7:66148400-66159000	Weak transcription	Placenta	Placenta
21	chr7:66148400-66159000	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr7:66148400-66159200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr7:66148400-66161600	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr7:66148400-66161600	Weak transcription	Brain Substantia Nigra	brain
25	chr7:66148400-66161800	Weak transcription	Brain Cingulate Gyrus	brain
26	chr7:66148400-66161800	Weak transcription	Colon Smooth Muscle	Colon
27	chr7:66148400-66178400	Weak transcription	Duodenum Mucosa	Duodenum
28	chr7:66148400-66182400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr7:66148400-66184400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr7:66148400-66184800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr7:66148600-66157200	Weak transcription	Fetal Stomach	stomach
32	chr7:66148600-66157800	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr7:66148600-66157800	Weak transcription	Stomach Smooth Muscle	stomach
34	chr7:66148600-66157800	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr7:66148600-66158600	Weak transcription	HSMMtube	muscle
36	chr7:66148600-66161800	Weak transcription	Brain Angular Gyrus	brain
37	chr7:66148600-66161800	Weak transcription	NH-A	brain
38	chr7:66148600-66172400	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr7:66148600-66177400	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr7:66149000-66157200	Weak transcription	Fetal Brain Female	brain
41	chr7:66149000-66157600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr7:66149000-66177600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr7:66149000-66199600	Weak transcription	Thymus	Thymus
44	chr7:66149200-66157400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr7:66149200-66159000	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr7:66149200-66161800	Weak transcription	Brain Hippocampus Middle	brain
47	chr7:66149400-66157400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr7:66149400-66157400	Weak transcription	Lung	lung
49	chr7:66149400-66157800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr7:66149600-66157200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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