Variant report

Variant	rs12596036
Chromosome Location	chr16:12205460-12205461
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11075050	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11075051	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11075052	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11640920	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11641707	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11643720	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11647573	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12596081	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12596229	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12597440	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12597662	0.87[ASN][1000 genomes]
rs16958983	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4074264	0.93[ASN][1000 genomes]
rs55693041	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55906538	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55925548	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55937851	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55975708	0.87[AMR][1000 genomes]
rs56058313	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56225320	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57288594	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs58198539	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59506769	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59855210	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7189640	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7190611	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73519857	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8051768	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8053242	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[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	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
2	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
3	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
4	nsv977111	chr16:12161129-12220593	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1039492	chr16:12176517-12210702	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv571460	chr16:12181702-12238602	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1052973	chr16:12188092-12307880	ZNF genes & repeats Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12184400-12231200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr16:12186800-12213400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr16:12189800-12209600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr16:12189800-12220400	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr16:12190000-12220200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr16:12190000-12220400	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr16:12190200-12210600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr16:12190800-12210600	Weak transcription	Pancreas	Pancrea
9	chr16:12191200-12223200	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr16:12191400-12213600	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr16:12191800-12207800	Weak transcription	Osteobl	bone
12	chr16:12192000-12206000	Weak transcription	Brain Substantia Nigra	brain
13	chr16:12192000-12213800	Weak transcription	Rectal Smooth Muscle	rectum
14	chr16:12192000-12214600	Weak transcription	Right Atrium	heart
15	chr16:12192200-12207200	Weak transcription	HSMMtube	muscle
16	chr16:12192400-12206400	Weak transcription	Brain Hippocampus Middle	brain
17	chr16:12192400-12210400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr16:12192400-12213200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr16:12192400-12213200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr16:12192800-12207000	Weak transcription	Brain Cingulate Gyrus	brain
21	chr16:12192800-12213600	Weak transcription	Adipose Nuclei	Adipose
22	chr16:12193000-12207000	Weak transcription	Fetal Thymus	thymus
23	chr16:12193000-12207600	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr16:12193800-12207000	Weak transcription	Esophagus	oesophagus
25	chr16:12193800-12207400	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr16:12194000-12212600	Weak transcription	Ovary	ovary
27	chr16:12194000-12213000	Weak transcription	Right Ventricle	heart
28	chr16:12194000-12215200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr16:12194200-12210600	Weak transcription	NHEK	skin
30	chr16:12198200-12227800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr16:12198600-12206200	Strong transcription	Primary B cells from peripheral blood	blood
32	chr16:12200200-12220200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr16:12200400-12206000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr16:12200400-12207400	Weak transcription	Spleen	Spleen
35	chr16:12200400-12209200	Weak transcription	Gastric	stomach
36	chr16:12200400-12210600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr16:12200400-12210600	Weak transcription	Aorta	Aorta
38	chr16:12200600-12206600	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr16:12200600-12210400	Weak transcription	Lung	lung
40	chr16:12200600-12213000	Weak transcription	Fetal Heart	heart
41	chr16:12200600-12215400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr16:12201000-12209200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr16:12201000-12210400	Weak transcription	Thymus	Thymus
44	chr16:12202000-12209400	Weak transcription	GM12878-XiMat	blood
45	chr16:12202600-12207200	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr16:12203400-12206800	Enhancers	HepG2	liver
47	chr16:12204000-12205800	Enhancers	Liver	Liver
48	chr16:12204400-12207400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr16:12204600-12208400	Enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr16:12204800-12206800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links