Variant report

Variant	rs350272
Chromosome Location	chr16:12234773-12234774
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs12598569	0.81[YRI][hapmap]
rs1632455	0.81[YRI][hapmap]
rs1641850	0.82[CHB][hapmap]
rs1641855	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs168414	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1704112	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1704116	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs183008	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs183010	0.81[EUR][1000 genomes]
rs193252	0.82[EUR][1000 genomes]
rs2664186	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs350203	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs350207	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs350209	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs350210	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs350226	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs350245	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs350248	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs350251	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs350252	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs350254	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs350255	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs350256	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs350271	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs350274	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs350275	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs350277	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs350278	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs350279	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs350285	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs350287	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4781187	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9922788	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	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
5	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
6	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
7	nsv528952	chr16:12222064-12234877	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs350272	ERCC4	cis	cerebellum	SCAN
rs350272	PARN	cis	cerebellum	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12213800-12255400	Weak transcription	Gastric	stomach
2	chr16:12215400-12241600	Weak transcription	NH-A	brain
3	chr16:12217800-12241800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr16:12218600-12241200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr16:12218800-12241000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr16:12219400-12237600	Weak transcription	Fetal Intestine Large	intestine
7	chr16:12220000-12236400	Strong transcription	Primary B cells from peripheral blood	blood
8	chr16:12220400-12236000	Strong transcription	Primary B cells from cord blood	blood
9	chr16:12220600-12236800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr16:12221000-12237200	Weak transcription	K562	blood
11	chr16:12221400-12236200	Strong transcription	GM12878-XiMat	blood
12	chr16:12221400-12236400	Strong transcription	Primary T cells from cord blood	blood
13	chr16:12221600-12241600	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr16:12222000-12240800	Weak transcription	Brain Anterior Caudate	brain
15	chr16:12227000-12234800	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr16:12227000-12235800	Weak transcription	Right Atrium	heart
17	chr16:12227600-12247000	Weak transcription	Colon Smooth Muscle	Colon
18	chr16:12228000-12236200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr16:12228600-12235600	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr16:12228600-12239600	Weak transcription	HSMMtube	muscle
21	chr16:12228600-12240800	Weak transcription	HSMM	muscle
22	chr16:12228600-12241400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr16:12228600-12243600	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr16:12228800-12236000	Weak transcription	Fetal Intestine Small	intestine
25	chr16:12228800-12239800	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr16:12228800-12240800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr16:12229000-12249000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr16:12229200-12236800	Weak transcription	A549	lung
29	chr16:12229200-12241000	Weak transcription	Fetal Kidney	kidney
30	chr16:12229400-12240800	Weak transcription	Primary hematopoietic stem cells	blood
31	chr16:12229400-12241000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr16:12229400-12241200	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr16:12229400-12242800	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr16:12229400-12248000	Weak transcription	Rectal Smooth Muscle	rectum
35	chr16:12229400-12250600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr16:12229800-12236000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr16:12229800-12241400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr16:12229800-12241400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr16:12229800-12244400	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr16:12229800-12251400	Weak transcription	NHEK	skin
41	chr16:12229800-12253600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr16:12230000-12237400	Weak transcription	Dnd41	blood
43	chr16:12230000-12240800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr16:12230000-12245600	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr16:12230200-12241200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr16:12230200-12241800	Weak transcription	Esophagus	oesophagus
47	chr16:12230200-12242000	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr16:12230200-12256200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr16:12230400-12239800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr16:12230600-12240800	Weak transcription	Primary T cells fromperipheralblood	blood

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