Variant report

Variant	rs16956738
Chromosome Location	chr15:31736231-31736232
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:31723431..31726207-chr15:31734992..31737659,2	K562	blood:
2	chr15:31732939..31734910-chr15:31736139..31739107,2	MCF-7	breast:

Extended variants
information (count: 42 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1075232	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12437749	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12437800	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12438318	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12438813	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12439239	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12439853	0.94[AMR][1000 genomes]
rs12440108	0.81[ASN][1000 genomes]
rs12441163	0.81[ASN][1000 genomes]
rs16956707	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes]
rs16956797	0.81[ASN][1000 genomes]
rs16956801	0.81[ASN][1000 genomes]
rs34959140	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4450360	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56249651	0.90[ASN][1000 genomes]
rs56396205	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs57491435	0.81[ASN][1000 genomes]
rs57924788	0.92[ASN][1000 genomes]
rs58156651	0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs66581165	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67216354	0.90[ASN][1000 genomes]
rs67634762	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67699697	0.90[ASN][1000 genomes]
rs7166243	0.81[ASN][1000 genomes]
rs72722829	0.94[AMR][1000 genomes]
rs72722847	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72722861	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72724938	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72724958	0.92[ASN][1000 genomes]
rs72724993	0.81[ASN][1000 genomes]
rs72724997	0.81[ASN][1000 genomes]
rs9672214	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9672538	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs16956738	CHRNA7	cis	Whole Blood	GTEx
rs16956738	CHRNA7	cis	Thyroid	GTEx
rs16956738	CTD-3092A11.2	cis	lung	GTEx
rs16956738	RP11-932O9.7	cis	lung	GTEx
rs16956738	RP11-932O9.7	cis	Artery Tibial	GTEx
rs16956738	CTD-3092A11.2	cis	Whole Blood	GTEx
rs16956738	CHRFAM7A	cis	multi-tissue	Pritchard
rs16956738	CHRNA7	cis	lung	GTEx
rs16956738	CHRNA7	cis	Artery Tibial	GTEx

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:31732800-31737400	Enhancers	NHDF-Ad	bronchial
2	chr15:31733400-31736600	Enhancers	NHLF	lung
3	chr15:31733400-31741000	Weak transcription	Spleen	Spleen
4	chr15:31733600-31736400	Enhancers	HUVEC	blood vessel
5	chr15:31733600-31736600	Enhancers	Muscle Satellite Cultured Cells	--
6	chr15:31733600-31736800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr15:31733600-31738000	Enhancers	GM12878-XiMat	blood
8	chr15:31733800-31736400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr15:31733800-31736400	Enhancers	HSMM	muscle
10	chr15:31733800-31736400	Enhancers	NH-A	brain
11	chr15:31733800-31736600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr15:31733800-31737000	Enhancers	Monocytes-CD14+_RO01746	blood
13	chr15:31733800-31741800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr15:31734200-31736400	Enhancers	HMEC	breast
15	chr15:31734200-31740400	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr15:31734200-31740800	Weak transcription	Placenta	Placenta
17	chr15:31734200-31740800	Weak transcription	Stomach Mucosa	stomach
18	chr15:31734400-31736600	Enhancers	Hela-S3	cervix
19	chr15:31734400-31740200	Weak transcription	Esophagus	oesophagus
20	chr15:31734400-31740600	Weak transcription	Adipose Nuclei	Adipose
21	chr15:31734400-31740800	Weak transcription	Fetal Thymus	thymus
22	chr15:31734400-31750000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr15:31734600-31736400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr15:31734600-31737000	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr15:31734600-31740600	Weak transcription	Primary T cells from cord blood	blood
26	chr15:31734600-31741200	Weak transcription	Gastric	stomach
27	chr15:31734800-31736600	Enhancers	A549	lung
28	chr15:31735200-31736600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr15:31735200-31736600	Enhancers	Osteobl	bone
30	chr15:31735400-31736400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr15:31735400-31736600	Enhancers	NHEK	skin
32	chr15:31735400-31740600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr15:31735400-31741000	Weak transcription	HSMMtube	muscle
34	chr15:31735600-31736400	Enhancers	Primary B cells from peripheral blood	blood
35	chr15:31735600-31736600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr15:31735600-31736600	Enhancers	Small Intestine	intestine
37	chr15:31735600-31736800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
38	chr15:31735800-31736400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr15:31735800-31736400	Enhancers	Primary hematopoietic stem cells	blood
40	chr15:31735800-31736400	Enhancers	Sigmoid Colon	Sigmoid Colon
41	chr15:31735800-31736600	Enhancers	Primary neutrophils fromperipheralblood	blood
42	chr15:31735800-31736600	Enhancers	Duodenum Mucosa	Duodenum
43	chr15:31735800-31736800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr15:31736000-31736400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
45	chr15:31736000-31736400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr15:31736000-31736600	Enhancers	Rectal Mucosa Donor 31	rectum
47	chr15:31736200-31736400	Enhancers	ES-I3 Cell Line	embryonic stem cell
48	chr15:31736200-31736600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr15:31736200-31736600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr15:31736200-31736600	Enhancers	Primary T cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links