Variant report

Variant	rs16959254
Chromosome Location	chr16:12435782-12435783
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	chr16:12433483..12435044-chr16:12435490..12437605,2	K562	blood:
2	chr16:12426504..12430184-chr16:12432340..12435917,5	K562	blood:

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10518185	1.00[CEU][hapmap];0.84[CHB][hapmap];0.88[EUR][1000 genomes]
rs11075063	0.96[EUR][1000 genomes]
rs11859773	1.00[CEU][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs11861545	1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.96[EUR][1000 genomes]
rs11866191	0.96[EUR][1000 genomes]
rs12102413	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12102589	0.86[ASW][hapmap];1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12103039	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13336090	1.00[GIH][hapmap]
rs13336107	0.92[EUR][1000 genomes]
rs13338250	0.96[EUR][1000 genomes]
rs168831	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16959258	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17817646	0.96[EUR][1000 genomes]
rs2080495	0.81[AFR][1000 genomes]
rs2432631	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2432632	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28469469	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28540294	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28561752	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28594525	0.89[EUR][1000 genomes]
rs28637093	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs289671	0.84[AFR][1000 genomes]
rs31678	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35413938	0.88[EUR][1000 genomes]
rs42672	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57739236	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58009694	0.85[EUR][1000 genomes]
rs60161095	0.92[EUR][1000 genomes]
rs60467313	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60642545	0.92[EUR][1000 genomes]
rs7195034	1.00[CEU][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes]
rs8053492	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs8061507	0.96[EUR][1000 genomes]
rs9922297	0.96[EUR][1000 genomes]
rs9924462	0.96[EUR][1000 genomes]
rs9928921	0.89[EUR][1000 genomes]
rs9929299	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9932979	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9944311	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9944312	0.87[AMR][1000 genomes];0.92[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	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
8	nsv905349	chr16:12408750-12445863	Flanking Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv571464	chr16:12423557-12449778	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12371400-12456800	Weak transcription	Aorta	Aorta
2	chr16:12405600-12442400	Weak transcription	Spleen	Spleen
3	chr16:12410000-12456600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr16:12410200-12464800	Weak transcription	Gastric	stomach
5	chr16:12416800-12438600	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr16:12418400-12438400	Weak transcription	Brain Anterior Caudate	brain
7	chr16:12425200-12442200	Weak transcription	Psoas Muscle	Psoas
8	chr16:12425400-12442000	Weak transcription	GM12878-XiMat	blood
9	chr16:12426800-12447200	Weak transcription	Lung	lung
10	chr16:12428400-12442400	Weak transcription	Primary hematopoietic stem cells	blood
11	chr16:12428400-12461200	Weak transcription	Thymus	Thymus
12	chr16:12430400-12436600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr16:12432400-12436800	Weak transcription	Fetal Heart	heart
14	chr16:12432400-12437200	Weak transcription	Primary B cells from cord blood	blood
15	chr16:12432600-12438600	Weak transcription	Adipose Nuclei	Adipose
16	chr16:12433000-12437200	Weak transcription	Fetal Brain Male	brain
17	chr16:12433200-12436000	Enhancers	NHDF-Ad	bronchial
18	chr16:12433200-12436000	Enhancers	NHLF	lung
19	chr16:12433200-12436200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr16:12433400-12435800	Enhancers	HSMM	muscle
21	chr16:12433400-12436000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr16:12433400-12436200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr16:12433400-12436200	Enhancers	NHEK	skin
24	chr16:12433600-12435800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr16:12433600-12435800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr16:12433600-12435800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr16:12433600-12435800	Enhancers	HSMMtube	muscle
28	chr16:12433600-12436000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr16:12433600-12436200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr16:12433600-12436200	Enhancers	HUVEC	blood vessel
31	chr16:12433800-12436000	Enhancers	Muscle Satellite Cultured Cells	--
32	chr16:12433800-12438200	Weak transcription	Brain Cingulate Gyrus	brain
33	chr16:12433800-12438800	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr16:12434000-12436000	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr16:12434000-12436600	Weak transcription	Colon Smooth Muscle	Colon
36	chr16:12434000-12436600	Weak transcription	Fetal Muscle Trunk	muscle
37	chr16:12434200-12435800	Enhancers	Esophagus	oesophagus
38	chr16:12434200-12436000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr16:12434200-12436600	Weak transcription	Stomach Smooth Muscle	stomach
40	chr16:12434200-12438200	Weak transcription	Brain Substantia Nigra	brain
41	chr16:12434400-12435800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr16:12434400-12436200	Enhancers	Osteobl	bone
43	chr16:12434400-12439200	Weak transcription	Brain Hippocampus Middle	brain
44	chr16:12434400-12450600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr16:12434600-12436000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr16:12434600-12438200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr16:12434600-12460200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr16:12434800-12435800	Enhancers	NH-A	brain
49	chr16:12434800-12436000	Enhancers	Fetal Muscle Leg	muscle
50	chr16:12434800-12436000	Enhancers	Hela-S3	cervix

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