Variant report

Variant	rs12439853
Chromosome Location	chr15:31634743-31634744
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10438322	0.81[CHD][hapmap];0.85[JPT][hapmap]
rs1075232	0.89[AMR][1000 genomes]
rs12437749	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12437800	1.00[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12437996	0.85[JPT][hapmap]
rs12438318	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12438813	0.91[AMR][1000 genomes]
rs12439239	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1370062	0.81[CHD][hapmap];0.85[JPT][hapmap]
rs16956707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16956738	0.94[AMR][1000 genomes]
rs1972825	0.85[JPT][hapmap]
rs34959140	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3743235	1.00[GIH][hapmap];0.85[JPT][hapmap]
rs4450360	0.94[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs56396205	0.94[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs58156651	0.82[AMR][1000 genomes]
rs6493531	0.85[JPT][hapmap]
rs66501706	0.88[ASN][1000 genomes]
rs66581165	0.84[AMR][1000 genomes]
rs67634762	0.84[AMR][1000 genomes]
rs72722829	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72722847	0.94[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs72722861	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72724938	0.86[AMR][1000 genomes]
rs9672214	0.94[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9672538	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 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	nsv903838	chr15:31452911-31672128	Strong transcription Flanking Active TSS Enhancers Genic enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	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
7	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
8	nsv456747	chr15:31537496-31637996	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv568772	chr15:31537496-31637996	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	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
11	esv1839818	chr15:31594828-31637996	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
12	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
13	nsv1048082	chr15:31610245-31667000	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
14	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
15	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
16	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
17	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
18	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
19	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
20	nsv1052942	chr15:31624164-31653633	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
21	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

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs12439853	CHRNA7	cis	Thyroid	GTEx
rs12439853	CHRNA7	cis	lung	GTEx
rs12439853	RP11-932O9.9	cis	Esophagus Muscularis	GTEx
rs12439853	RP11-932O9.7	cis	lung	GTEx
rs12439853	CTD-3092A11.2	cis	lung	GTEx
rs12439853	CHRFAM7A	cis	multi-tissue	Pritchard
rs12439853	CTD-3092A11.2	cis	Artery Tibial	GTEx
rs12439853	RP11-932O9.7	cis	Artery Tibial	GTEx
rs12439853	GOLGA8R	cis	Heart Left Ventricle	GTEx
rs12439853	CTD-3092A11.2	cis	Whole Blood	GTEx
rs12439853	CHRNA7	cis	Artery Tibial	GTEx
rs12439853	CHRNA7	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:31621600-31637200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:31621800-31636000	Enhancers	Small Intestine	intestine
3	chr15:31621800-31637600	Enhancers	Psoas Muscle	Psoas
4	chr15:31622000-31637600	Enhancers	Left Ventricle	heart
5	chr15:31622600-31640200	Enhancers	Pancreas	Pancrea
6	chr15:31622800-31657400	Enhancers	Right Atrium	heart
7	chr15:31623400-31637200	Enhancers	Liver	Liver
8	chr15:31624400-31634800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr15:31624400-31635200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr15:31625200-31649000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr15:31626000-31638400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr15:31626400-31638400	Enhancers	Fetal Muscle Trunk	muscle
13	chr15:31626600-31638400	Genic enhancers	Fetal Thymus	thymus
14	chr15:31627000-31637600	Enhancers	Colon Smooth Muscle	Colon
15	chr15:31627200-31635000	Genic enhancers	Primary B cells from peripheral blood	blood
16	chr15:31627200-31635200	Enhancers	Colonic Mucosa	Colon
17	chr15:31627200-31643000	Genic enhancers	Spleen	Spleen
18	chr15:31628200-31635200	Enhancers	Brain Germinal Matrix	brain
19	chr15:31629000-31638200	Enhancers	Fetal Brain Male	brain
20	chr15:31631000-31635600	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr15:31631200-31634800	Genic enhancers	Primary T cells from cord blood	blood
22	chr15:31631200-31635400	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr15:31631200-31635600	Strong transcription	Dnd41	blood
24	chr15:31631400-31635200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr15:31631400-31635400	Weak transcription	Hela-S3	cervix
26	chr15:31631400-31636200	Genic enhancers	Monocytes-CD14+_RO01746	blood
27	chr15:31631400-31644400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr15:31631400-31645000	Enhancers	Brain Substantia Nigra	brain
29	chr15:31631600-31634800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
30	chr15:31631600-31634800	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
31	chr15:31631600-31644600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr15:31631800-31635400	Genic enhancers	Primary monocytes fromperipheralblood	blood
33	chr15:31631800-31635400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr15:31631800-31636200	Enhancers	Brain Anterior Caudate	brain
35	chr15:31631800-31636400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr15:31631800-31637600	Weak transcription	A549	lung
37	chr15:31632000-31636200	Weak transcription	Aorta	Aorta
38	chr15:31632200-31636000	Weak transcription	NHDF-Ad	bronchial
39	chr15:31632200-31636400	Weak transcription	HepG2	liver
40	chr15:31632200-31638400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr15:31632200-31639000	Enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr15:31632200-31644400	Weak transcription	NH-A	brain
43	chr15:31632400-31635200	Weak transcription	Fetal Intestine Large	intestine
44	chr15:31632400-31636000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr15:31632400-31636600	Enhancers	Duodenum Smooth Muscle	Duodenum
46	chr15:31632400-31636600	Weak transcription	HSMMtube	muscle
47	chr15:31632400-31637000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr15:31632400-31637200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr15:31632400-31637200	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr15:31632400-31637600	Enhancers	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links