Variant report

Variant	rs7190509
Chromosome Location	chr16:12449855-12449856
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11075061	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11075062	0.88[GIH][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes]
rs11645864	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11648255	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11648926	0.85[EUR][1000 genomes]
rs12102400	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12102608	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12445569	0.82[EUR][1000 genomes]
rs12448443	0.80[EUR][1000 genomes]
rs16959318	0.90[EUR][1000 genomes]
rs176717	0.82[EUR][1000 genomes]
rs209846	0.91[EUR][1000 genomes]
rs209849	0.83[EUR][1000 genomes]
rs209850	0.83[EUR][1000 genomes]
rs209851	0.84[EUR][1000 genomes]
rs209853	0.85[EUR][1000 genomes]
rs209855	0.83[EUR][1000 genomes]
rs209856	0.86[EUR][1000 genomes]
rs289673	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs31679	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35818743	0.80[EUR][1000 genomes]
rs476267	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4780422	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4780423	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4781201	0.82[EUR][1000 genomes]
rs4781207	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4781208	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4781209	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4781211	0.84[EUR][1000 genomes]
rs4781214	0.85[GIH][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs544598	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62039994	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6498277	0.83[EUR][1000 genomes]
rs6498278	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6498279	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7184477	0.94[EUR][1000 genomes]
rs7189945	0.81[EUR][1000 genomes]
rs7195024	0.88[CEU][hapmap]
rs7195981	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7199556	0.81[EUR][1000 genomes]
rs7201621	0.92[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7202201	0.82[EUR][1000 genomes]
rs7203117	0.82[EUR][1000 genomes]
rs8051758	0.81[EUR][1000 genomes]
rs868773	0.81[CEU][hapmap];0.88[GIH][hapmap];0.80[TSI][hapmap]
rs9284322	0.95[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9302469	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9939036	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv833141	chr16:12314613-12487992	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv457411	chr16:12363304-12520199	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv571462	chr16:12363304-12520199	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv571463	chr16:12367791-12783535	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv1045385	chr16:12376389-12517006	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv542748	chr16:12376389-12517006	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7190509	C16orf63	cis	parietal	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12371400-12456800	Weak transcription	Aorta	Aorta
2	chr16:12410000-12456600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr16:12410200-12464800	Weak transcription	Gastric	stomach
4	chr16:12428400-12461200	Weak transcription	Thymus	Thymus
5	chr16:12434400-12450600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr16:12434600-12460200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr16:12435800-12454800	Weak transcription	Pancreas	Pancrea
8	chr16:12435800-12484000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr16:12436000-12450000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr16:12436000-12452400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr16:12436200-12450000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr16:12436200-12456800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr16:12437400-12456600	Weak transcription	Rectal Smooth Muscle	rectum
14	chr16:12437600-12456200	Weak transcription	Right Atrium	heart
15	chr16:12438800-12456400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr16:12439000-12450000	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr16:12439200-12450000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr16:12439600-12452600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr16:12442600-12450600	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr16:12443000-12450800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr16:12443200-12452400	Weak transcription	GM12878-XiMat	blood
22	chr16:12443200-12454200	Weak transcription	Fetal Muscle Leg	muscle
23	chr16:12443200-12456600	Weak transcription	Spleen	Spleen
24	chr16:12443200-12456800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr16:12443200-12456800	Weak transcription	Psoas Muscle	Psoas
26	chr16:12443200-12456800	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr16:12443200-12457000	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr16:12443400-12452400	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr16:12443600-12470800	Weak transcription	HepG2	liver
30	chr16:12444000-12454800	Strong transcription	Primary T cells from cord blood	blood
31	chr16:12444800-12491400	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr16:12445200-12450000	Weak transcription	Fetal Thymus	thymus
33	chr16:12447000-12452000	Enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr16:12447400-12451000	Enhancers	Brain Inferior Temporal Lobe	brain
35	chr16:12447600-12452000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr16:12447600-12452400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr16:12447600-12453000	Weak transcription	Lung	lung
38	chr16:12447600-12456200	Weak transcription	Left Ventricle	heart
39	chr16:12447600-12456400	Weak transcription	Fetal Muscle Trunk	muscle
40	chr16:12447600-12456400	Weak transcription	Ovary	ovary
41	chr16:12447600-12470000	Weak transcription	Esophagus	oesophagus
42	chr16:12447800-12452000	Enhancers	Brain Substantia Nigra	brain
43	chr16:12448000-12451000	Enhancers	Brain Anterior Caudate	brain
44	chr16:12448000-12452000	Enhancers	Primary hematopoietic stem cells	blood
45	chr16:12448200-12450800	Enhancers	Brain Angular Gyrus	brain
46	chr16:12448400-12456600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr16:12448600-12452200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr16:12448600-12460400	Weak transcription	Fetal Stomach	stomach
49	chr16:12448600-12471200	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr16:12448800-12452000	Weak transcription	NHEK	skin

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