Variant report

Variant	rs9672538
Chromosome Location	chr15:31672152-31672153
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10438322	0.82[JPT][hapmap]
rs1075232	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12437749	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12437800	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12437996	0.82[JPT][hapmap]
rs12438318	0.85[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12438813	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12439239	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12439853	1.00[AMR][1000 genomes]
rs1370062	0.82[JPT][hapmap]
rs16956707	0.82[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes]
rs16956738	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1972825	0.82[JPT][hapmap]
rs34959140	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3743235	0.82[JPT][hapmap]
rs4450360	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56396205	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58156651	0.82[AMR][1000 genomes]
rs6493531	0.82[JPT][hapmap]
rs66581165	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs67634762	0.84[AMR][1000 genomes]
rs72722829	1.00[AMR][1000 genomes]
rs72722847	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72722861	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72724938	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9672214	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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	nsv1050482	chr15:31601016-31672921	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
9	nsv1045944	chr15:31610245-31672921	Enhancers Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
10	nsv516681	chr15:31616674-31675453	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS 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	13 gene(s)	inside rSNPs	diseases
11	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
12	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
13	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
14	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
15	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
16	nsv1051910	chr15:31641254-31672921	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs9672538	GOLGA8R	cis	Heart Left Ventricle	GTEx
rs9672538	CHRNA7	cis	Whole Blood	GTEx
rs9672538	RP11-932O9.7	cis	lung	GTEx
rs9672538	RP11-932O9.7	cis	Artery Tibial	GTEx
rs9672538	CHRNA7	cis	Thyroid	GTEx
rs9672538	CTD-3092A11.2	cis	Whole Blood	GTEx
rs9672538	CTD-3092A11.2	cis	Artery Tibial	GTEx
rs9672538	CHRNA7	cis	lung	GTEx
rs9672538	CTD-3092A11.2	cis	lung	GTEx
rs9672538	RP11-932O9.9	cis	Esophagus Muscularis	GTEx
rs9672538	CHRNA7	cis	Artery Tibial	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:31662000-31672600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr15:31663000-31674400	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr15:31663200-31675800	Strong transcription	Dnd41	blood
4	chr15:31663800-31673000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
5	chr15:31663800-31674600	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr15:31664000-31673200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr15:31664000-31674600	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr15:31664200-31672800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr15:31664200-31673800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr15:31664600-31672800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr15:31664600-31672800	Genic enhancers	Left Ventricle	heart
12	chr15:31664800-31679800	Weak transcription	Hela-S3	cervix
13	chr15:31665000-31673800	Strong transcription	Cortex derived primary cultured neurospheres	brain
14	chr15:31665000-31675600	Strong transcription	Brain Germinal Matrix	brain
15	chr15:31665400-31672200	Genic enhancers	Primary T helper cells PMA-I stimulated	--
16	chr15:31665400-31680000	Weak transcription	Ovary	ovary
17	chr15:31665600-31672600	Strong transcription	Fetal Stomach	stomach
18	chr15:31665800-31680000	Weak transcription	Fetal Lung	lung
19	chr15:31666000-31672600	Weak transcription	Colon Smooth Muscle	Colon
20	chr15:31666000-31675000	Strong transcription	Thymus	Thymus
21	chr15:31666000-31675600	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr15:31666000-31679400	Weak transcription	Stomach Mucosa	stomach
23	chr15:31666400-31673400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr15:31666600-31674400	Weak transcription	HepG2	liver
25	chr15:31666600-31674800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr15:31666800-31673000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr15:31666800-31673800	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr15:31666800-31675200	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr15:31667400-31673000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr15:31667400-31674400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr15:31667600-31674400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr15:31668000-31672600	Weak transcription	Primary hematopoietic stem cells	blood
33	chr15:31668000-31674600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr15:31668000-31675200	Strong transcription	Stomach Smooth Muscle	stomach
35	chr15:31668200-31674200	Strong transcription	Adipose Nuclei	Adipose
36	chr15:31668200-31675000	Strong transcription	Gastric	stomach
37	chr15:31668400-31672600	Weak transcription	NHLF	lung
38	chr15:31668400-31673200	Enhancers	Fetal Intestine Large	intestine
39	chr15:31668400-31677200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr15:31668800-31672600	Weak transcription	Fetal Kidney	kidney
41	chr15:31668800-31672800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr15:31669000-31672200	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr15:31669000-31679800	Weak transcription	GM12878-XiMat	blood
44	chr15:31669400-31675000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr15:31669400-31675800	Strong transcription	Spleen	Spleen
46	chr15:31669800-31672600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr15:31669800-31673200	Strong transcription	Pancreas	Pancrea
48	chr15:31669800-31674800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr15:31669800-31675000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr15:31669800-31675000	Weak transcription	H1 Cell Line	embryonic stem cell

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