Variant report

Variant	rs9922788
Chromosome Location	chr16:12243932-12243933
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	chr16:12235977..12239654-chr16:12243100..12246222,3	K562	blood:

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1641850	0.82[CHB][hapmap];0.84[AMR][1000 genomes]
rs1641855	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs168414	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1704112	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1704116	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs183008	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs193252	0.81[EUR][1000 genomes]
rs2664186	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs350203	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs350207	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs350209	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs350210	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs350226	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs350245	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs350248	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs350251	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs350252	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs350254	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs350255	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs350256	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs350271	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs350272	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs350274	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs350275	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs350277	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs350278	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs350279	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs350285	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs350287	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4781187	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
3	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
4	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
5	nsv1039590	chr16:12237623-12279574	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9922788	ERCC4	cis	cerebellum	SCAN
rs9922788	PARN	cis	cerebellum	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12213800-12255400	Weak transcription	Gastric	stomach
2	chr16:12227600-12247000	Weak transcription	Colon Smooth Muscle	Colon
3	chr16:12229000-12249000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr16:12229400-12248000	Weak transcription	Rectal Smooth Muscle	rectum
5	chr16:12229400-12250600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr16:12229800-12244400	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr16:12229800-12251400	Weak transcription	NHEK	skin
8	chr16:12229800-12253600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr16:12230000-12245600	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr16:12230200-12256200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr16:12231400-12251000	Weak transcription	Ovary	ovary
12	chr16:12231400-12268000	Weak transcription	Pancreas	Pancrea
13	chr16:12232000-12248600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr16:12233600-12251000	Weak transcription	NHDF-Ad	bronchial
15	chr16:12234600-12244000	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr16:12234600-12247600	Weak transcription	Stomach Smooth Muscle	stomach
17	chr16:12234600-12248600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr16:12234600-12261600	Weak transcription	Aorta	Aorta
19	chr16:12234600-12265600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr16:12235400-12251000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr16:12236200-12249400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr16:12236200-12250800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr16:12237800-12249600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr16:12241200-12245600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr16:12241400-12245600	Enhancers	Fetal Thymus	thymus
26	chr16:12241600-12246200	Enhancers	HepG2	liver
27	chr16:12242000-12244000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr16:12242200-12244000	Weak transcription	Spleen	Spleen
29	chr16:12242200-12246400	Weak transcription	Brain Angular Gyrus	brain
30	chr16:12242200-12248200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr16:12242200-12248800	Weak transcription	Adipose Nuclei	Adipose
32	chr16:12242200-12251000	Weak transcription	HSMMtube	muscle
33	chr16:12242200-12252400	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr16:12242200-12252400	Weak transcription	Left Ventricle	heart
35	chr16:12242200-12252600	Weak transcription	Brain Cingulate Gyrus	brain
36	chr16:12242200-12252600	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr16:12242200-12253800	Weak transcription	Right Atrium	heart
38	chr16:12242200-12255200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr16:12242200-12261600	Weak transcription	Lung	lung
40	chr16:12242200-12262800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr16:12242200-12299400	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr16:12242400-12244200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr16:12242400-12244200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr16:12242400-12244200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr16:12242400-12244400	Weak transcription	Primary hematopoietic stem cells	blood
46	chr16:12242400-12245000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr16:12242400-12246200	Weak transcription	Brain Hippocampus Middle	brain
48	chr16:12242400-12247000	Weak transcription	Fetal Stomach	stomach
49	chr16:12242400-12250600	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr16:12242400-12252400	Weak transcription	Right Ventricle	heart

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