Variant report

Variant	rs7197059
Chromosome Location	chr16:12103668-12103669
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11075041	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11639821	0.89[CEU][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11641950	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11644227	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11859213	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11859801	1.00[CHD][hapmap]
rs11862467	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13334063	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2865105	0.96[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap]
rs3844112	1.00[CEU][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3916255	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs417938	0.95[MEX][hapmap]
rs436838	0.86[MEX][hapmap]
rs442234	0.91[MEX][hapmap]
rs55995758	0.82[EUR][1000 genomes]
rs59446863	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62037701	0.95[ASN][1000 genomes]
rs6498260	0.89[CEU][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6498261	0.89[CEU][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6498262	0.89[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7206768	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8044943	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8045634	0.86[MEX][hapmap]
rs8050827	0.82[MEX][hapmap]
rs8051012	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8051298	1.00[CHD][hapmap];0.87[YRI][hapmap]
rs8060439	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9929844	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042660	chr16:11846873-12110435	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv905347	chr16:12010444-12243329	Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
3	nsv1043096	chr16:12013915-12840769	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv482458	chr16:12014925-12145977	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers 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	23 gene(s)	inside rSNPs	diseases
5	nsv1043959	chr16:12039346-12285269	Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	nsv984259	chr16:12092609-12104575	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7197059	RP11-166B2.1	cis	Skin Sun Exposed Lower leg	GTEx
rs7197059	GAB3	trans	parietal	SCAN
rs7197059	GSPT1	cis	parietal	SCAN
rs7197059	TNFRSF17	cis	parietal	SCAN
rs7197059	TNFRSF17	cis	cerebellum	SCAN

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12071400-12130800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr16:12071800-12140200	Weak transcription	Fetal Intestine Small	intestine
3	chr16:12072400-12104400	Weak transcription	NHLF	lung
4	chr16:12079600-12109600	Weak transcription	Gastric	stomach
5	chr16:12085400-12118200	Weak transcription	Esophagus	oesophagus
6	chr16:12088600-12104200	Weak transcription	Right Ventricle	heart
7	chr16:12088600-12109200	Weak transcription	Fetal Kidney	kidney
8	chr16:12088600-12110000	Weak transcription	NH-A	brain
9	chr16:12088800-12106600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr16:12088800-12108200	Weak transcription	Fetal Muscle Trunk	muscle
11	chr16:12088800-12115400	Weak transcription	Placenta	Placenta
12	chr16:12089000-12104400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr16:12092400-12105600	Weak transcription	Rectal Smooth Muscle	rectum
14	chr16:12092400-12110200	Weak transcription	NHEK	skin
15	chr16:12092600-12107800	Weak transcription	Liver	Liver
16	chr16:12093200-12103800	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr16:12093400-12104000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr16:12094200-12103800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr16:12094200-12105600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr16:12094200-12110000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr16:12094800-12104200	Weak transcription	Left Ventricle	heart
22	chr16:12095000-12103800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr16:12096800-12103800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr16:12096800-12104000	Weak transcription	NHDF-Ad	bronchial
25	chr16:12096800-12110000	Weak transcription	Osteobl	bone
26	chr16:12096800-12111800	Weak transcription	Ovary	ovary
27	chr16:12097000-12107800	Weak transcription	Fetal Lung	lung
28	chr16:12097000-12109400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr16:12097200-12104600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr16:12097200-12107800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr16:12097600-12110200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr16:12098400-12136000	Weak transcription	Fetal Stomach	stomach
33	chr16:12098600-12109400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr16:12098600-12118200	Weak transcription	Pancreas	Pancrea
35	chr16:12099000-12109400	Weak transcription	Brain Germinal Matrix	brain
36	chr16:12099400-12108200	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr16:12099400-12118400	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr16:12099600-12103800	Weak transcription	Adipose Nuclei	Adipose
39	chr16:12099600-12104600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr16:12099600-12111800	Weak transcription	Fetal Muscle Leg	muscle
41	chr16:12099600-12112600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr16:12099600-12135200	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr16:12099600-12141200	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr16:12099800-12104000	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr16:12099800-12104400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr16:12101000-12104200	Weak transcription	K562	blood
47	chr16:12101400-12110200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr16:12101800-12103800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr16:12101800-12103800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr16:12101800-12110000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links