Variant report

Variant	rs8053242
Chromosome Location	chr16:12212623-12212624
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:12207504..12209871-chr16:12211621..12214983,3	K562	blood:
2	chr16:12212007..12215167-chr16:12222860..12225449,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000048471	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11075050	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11075051	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11075052	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11640920	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11641707	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11643720	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11647573	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12596036	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12596081	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12596229	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12597440	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12597662	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16958983	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs350244	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs4074264	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55693041	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55906538	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55925548	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55937851	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55975708	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56058313	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56225320	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57288594	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58198539	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59506769	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59855210	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6498266	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7189640	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7190611	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73519857	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8051768	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[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	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
6	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
7	nsv1042146	chr16:12208242-12256699	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs8053242	PLA2G10	cis	parietal	SCAN

Chromatin state (count:74 , 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	chr16:12189800-12220400	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr16:12190000-12220200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr16:12190000-12220400	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr16:12191200-12223200	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr16:12191400-12213600	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr16:12192000-12213800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr16:12192000-12214600	Weak transcription	Right Atrium	heart
10	chr16:12192400-12213200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr16:12192400-12213200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr16:12192800-12213600	Weak transcription	Adipose Nuclei	Adipose
13	chr16:12194000-12213000	Weak transcription	Right Ventricle	heart
14	chr16:12194000-12215200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr16:12198200-12227800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr16:12200200-12220200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr16:12200600-12213000	Weak transcription	Fetal Heart	heart
18	chr16:12200600-12215400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr16:12204800-12222000	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr16:12205400-12213400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr16:12205800-12213600	Weak transcription	Stomach Smooth Muscle	stomach
22	chr16:12207200-12213000	Weak transcription	Placenta	Placenta
23	chr16:12207200-12218400	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr16:12208000-12221200	Weak transcription	Brain Substantia Nigra	brain
25	chr16:12208200-12212800	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr16:12208200-12213000	Weak transcription	Fetal Muscle Leg	muscle
27	chr16:12208200-12213400	Weak transcription	Brain Hippocampus Middle	brain
28	chr16:12208200-12228000	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr16:12208400-12212800	Weak transcription	NHDF-Ad	bronchial
30	chr16:12208400-12213000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr16:12208400-12213000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr16:12208400-12213000	Weak transcription	HSMM	muscle
33	chr16:12208400-12213400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr16:12208400-12213400	Weak transcription	Osteobl	bone
35	chr16:12208400-12213600	Weak transcription	Brain Cingulate Gyrus	brain
36	chr16:12208400-12213800	Weak transcription	Brain Angular Gyrus	brain
37	chr16:12208400-12214200	Weak transcription	Fetal Brain Female	brain
38	chr16:12208400-12218400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr16:12208400-12218800	Weak transcription	Brain Anterior Caudate	brain
40	chr16:12208600-12226800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr16:12208800-12213400	Strong transcription	Primary B cells from peripheral blood	blood
42	chr16:12209600-12213400	Weak transcription	Gastric	stomach
43	chr16:12209800-12212800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr16:12211000-12213000	Weak transcription	Lung	lung
45	chr16:12211000-12213200	Weak transcription	HSMMtube	muscle
46	chr16:12211000-12213400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr16:12211000-12213400	Weak transcription	NHEK	skin
48	chr16:12211000-12213600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr16:12211000-12218600	Weak transcription	Thymus	Thymus
50	chr16:12211000-12218600	Weak transcription	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links