Variant report

Variant	rs58156651
Chromosome Location	chr15:31749067-31749068
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NR3C1	chr15:31748696-31749357	A549	lung:	n/a	n/a
2	FOXA2	chr15:31749027-31749513	A549	lung:	n/a	n/a
3	SP1	chr15:31748963-31750246	A549	lung:	n/a	n/a
4	MAX	chr15:31749019-31750228	A549	lung:	n/a	chr15:31749603-31749616 chr15:31749605-31749614 chr15:31749600-31749619 chr15:31749604-31749615
5	TCF12	chr15:31749042-31750243	A549	lung:	n/a	chr15:31750160-31750167
6	POLR2A	chr15:31749030-31749134	MCF10A-Er-Src	breast:	n/a	n/a
7	FOXA2	chr15:31749007-31749540	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:31747904..31750478-chr15:31754531..31757245,2	MCF-7	breast:
2	chr15:31748477..31753108-chr15:31776889..31783172,7	MCF-7	breast:
3	chr15:31731861..31735385-chr15:31748681..31751856,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259696	TF binding region

Extended variants
information (count: 44 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1075232	0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11858516	0.81[ASN][1000 genomes]
rs12437749	0.82[AMR][1000 genomes]
rs12437800	0.82[AMR][1000 genomes]
rs12438318	0.87[AMR][1000 genomes]
rs12438813	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12439239	0.82[AMR][1000 genomes]
rs12439853	0.82[AMR][1000 genomes]
rs12440108	0.82[ASN][1000 genomes]
rs12441163	0.82[ASN][1000 genomes]
rs16956707	0.82[AMR][1000 genomes]
rs16956738	0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs16956797	0.82[ASN][1000 genomes]
rs16956801	0.82[ASN][1000 genomes]
rs34959140	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4450360	0.87[AMR][1000 genomes]
rs56249651	0.98[ASN][1000 genomes]
rs56396205	0.87[AMR][1000 genomes]
rs57491435	0.82[ASN][1000 genomes]
rs57924788	1.00[ASN][1000 genomes]
rs66581165	0.97[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs67216354	0.98[ASN][1000 genomes]
rs67634762	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs67699697	0.98[ASN][1000 genomes]
rs7166243	0.82[ASN][1000 genomes]
rs72722829	0.82[AMR][1000 genomes]
rs72722847	0.87[AMR][1000 genomes]
rs72722861	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs72724938	0.93[ASN][1000 genomes]
rs72724958	1.00[ASN][1000 genomes]
rs72724993	0.82[ASN][1000 genomes]
rs72724997	0.82[ASN][1000 genomes]
rs9672214	0.87[AMR][1000 genomes]
rs9672538	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	nsv1051589	chr15:31728004-31972706	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv542320	chr15:31728004-31972706	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv469633	chr15:31731003-31904613	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv482330	chr15:31731003-31904613	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv903844	chr15:31736091-31781988	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv1046271	chr15:31741255-31795961	Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs58156651	CHRNA7	cis	Whole Blood	GTEx
rs58156651	RP11-932O9.9	cis	Esophagus Muscularis	GTEx
rs58156651	CTD-3092A11.2	cis	lung	GTEx
rs58156651	CHRNA7	cis	lung	GTEx
rs58156651	RP11-932O9.9	cis	Skin Sun Exposed Lower leg	GTEx
rs58156651	CTD-3092A11.2	cis	Whole Blood	GTEx
rs58156651	RP11-932O9.7	cis	Artery Tibial	GTEx
rs58156651	CHRNA7	cis	Artery Tibial	GTEx

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:31734400-31750000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:31741400-31749400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr15:31745800-31750000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr15:31747000-31750800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr15:31748000-31749600	Weak transcription	Primary B cells from peripheral blood	blood
6	chr15:31748000-31751000	Weak transcription	Primary T cells from cord blood	blood
7	chr15:31748000-31751000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr15:31748200-31749200	Weak transcription	GM12878-XiMat	blood
9	chr15:31748200-31750400	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr15:31748200-31750800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr15:31748200-31750800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr15:31748200-31750800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr15:31748200-31751000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr15:31748200-31751000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr15:31748400-31751800	Enhancers	A549	lung
16	chr15:31748600-31751600	Enhancers	Esophagus	oesophagus
17	chr15:31748600-31751800	Enhancers	NHEK	skin
18	chr15:31748600-31752000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr15:31748800-31749200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr15:31748800-31749200	Enhancers	Osteobl	bone
21	chr15:31748800-31749400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr15:31748800-31749400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr15:31748800-31749400	Enhancers	Aorta	Aorta
24	chr15:31748800-31749400	Enhancers	NHDF-Ad	bronchial
25	chr15:31748800-31750600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr15:31748800-31750600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr15:31748800-31750800	Enhancers	Skeletal Muscle Male	skeletal muscle
28	chr15:31748800-31751000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr15:31748800-31751000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr15:31748800-31751200	Enhancers	Adipose Nuclei	Adipose
31	chr15:31748800-31751400	Enhancers	HSMM	muscle
32	chr15:31748800-31751400	Enhancers	HSMMtube	muscle
33	chr15:31749000-31749200	Enhancers	Colonic Mucosa	Colon
34	chr15:31749000-31749200	Enhancers	Left Ventricle	heart
35	chr15:31749000-31749200	Enhancers	Right Atrium	heart
36	chr15:31749000-31749600	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr15:31749000-31749800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr15:31749000-31750000	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr15:31749000-31750400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr15:31749000-31750600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
41	chr15:31749000-31750600	Bivalent Enhancer	Fetal Muscle Leg	muscle
42	chr15:31749000-31750600	Enhancers	NHLF	lung
43	chr15:31749000-31751800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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