Variant report

Variant	rs9672214
Chromosome Location	chr15:31677775-31677776
allele	A/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1075232	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12437749	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12437800	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12438318	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12438813	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12439239	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12439853	0.94[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs16956707	0.94[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs16956738	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34959140	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4450360	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56396205	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58156651	0.87[AMR][1000 genomes]
rs66581165	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs67634762	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs72722829	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72722847	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72722861	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72724938	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9672538	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv903831	chr15:30986051-31723279	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
2	nsv1054147	chr15:31014507-31972706	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv542306	chr15:31014507-31972706	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
4	nsv932896	chr15:31292475-31730445	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
5	esv1815415	chr15:31483843-31697213	Genic enhancers Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
6	esv34100	chr15:31496514-31792591	Active TSS Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
7	nsv903840	chr15:31589970-31800149	Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
8	nsv903841	chr15:31616674-31697242	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	nsv903842	chr15:31621321-31697242	Weak transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
10	nsv456748	chr15:31621321-31697642	Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
11	nsv568801	chr15:31621321-31697642	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
12	esv1810782	chr15:31633161-31697642	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
13	nsv903843	chr15:31672947-31723279	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs9672214	CTD-3092A11.2	cis	lung	GTEx
rs9672214	CTD-3092A11.2	cis	Artery Tibial	GTEx
rs9672214	CHRNA7	cis	Artery Tibial	GTEx
rs9672214	RP11-932O9.7	cis	Artery Tibial	GTEx
rs9672214	RP11-932O9.9	cis	Esophagus Muscularis	GTEx
rs9672214	CHRNA7	cis	Whole Blood	GTEx
rs9672214	CTD-3092A11.2	cis	Whole Blood	GTEx
rs9672214	GOLGA8R	cis	Heart Left Ventricle	GTEx
rs9672214	RP11-932O9.7	cis	lung	GTEx
rs9672214	CHRNA7	cis	Thyroid	GTEx
rs9672214	CHRNA7	cis	lung	GTEx

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:31664800-31679800	Weak transcription	Hela-S3	cervix
2	chr15:31665400-31680000	Weak transcription	Ovary	ovary
3	chr15:31665800-31680000	Weak transcription	Fetal Lung	lung
4	chr15:31666000-31679400	Weak transcription	Stomach Mucosa	stomach
5	chr15:31669000-31679800	Weak transcription	GM12878-XiMat	blood
6	chr15:31670800-31683800	Weak transcription	Small Intestine	intestine
7	chr15:31672200-31680000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr15:31672400-31679800	Weak transcription	Fetal Brain Male	brain
9	chr15:31672800-31679800	Weak transcription	Brain Angular Gyrus	brain
10	chr15:31673000-31679200	Weak transcription	Osteobl	bone
11	chr15:31673000-31680000	Weak transcription	Colon Smooth Muscle	Colon
12	chr15:31673200-31679400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr15:31673200-31679800	Weak transcription	Rectal Smooth Muscle	rectum
14	chr15:31673200-31680000	Weak transcription	Primary hematopoietic stem cells	blood
15	chr15:31673600-31679400	Weak transcription	NH-A	brain
16	chr15:31673600-31679800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr15:31673600-31684000	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr15:31673800-31679800	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr15:31673800-31679800	Weak transcription	Brain Substantia Nigra	brain
20	chr15:31673800-31680000	Weak transcription	Brain Anterior Caudate	brain
21	chr15:31674200-31679400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr15:31674200-31679800	Weak transcription	Brain Cingulate Gyrus	brain
23	chr15:31674200-31679800	Weak transcription	NHLF	lung
24	chr15:31674200-31680000	Weak transcription	Brain Hippocampus Middle	brain
25	chr15:31674200-31684000	Weak transcription	Colonic Mucosa	Colon
26	chr15:31674400-31677800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr15:31674400-31679000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr15:31674400-31679200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr15:31674400-31679400	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr15:31674400-31680000	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr15:31674600-31679400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr15:31674600-31679800	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr15:31674600-31679800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr15:31674600-31679800	Weak transcription	HSMMtube	muscle
35	chr15:31674600-31680000	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr15:31674600-31683800	Weak transcription	Primary B cells from peripheral blood	blood
37	chr15:31674600-31684000	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr15:31674800-31677800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr15:31674800-31679800	Weak transcription	Psoas Muscle	Psoas
40	chr15:31675000-31677800	Weak transcription	Thymus	Thymus
41	chr15:31675000-31678800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr15:31675000-31679400	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr15:31675000-31684000	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr15:31675200-31679200	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr15:31675200-31680000	Weak transcription	Fetal Muscle Trunk	muscle
46	chr15:31675200-31680000	Weak transcription	Stomach Smooth Muscle	stomach
47	chr15:31675200-31681600	Weak transcription	Fetal Stomach	stomach
48	chr15:31675200-31684000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr15:31675400-31678800	Weak transcription	Fetal Heart	heart
50	chr15:31675400-31679400	Weak transcription	Skeletal Muscle Female	skeletal muscle

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