Variant report

Variant	rs2270838
Chromosome Location	chr16:69959223-69959224
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAZ	chr16:69958614-69959467	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:69957939..69963004-chr16:69963560..69969238,6	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CLEC18A-1	chr16:69958915-69959387	NONHSAT143375

Variant related genes	Relation type
WWP2	TF binding region
ENSG00000198373	Chromatin interaction
ENSG00000208017	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs2133796	0.83[EUR][1000 genomes]
rs57613728	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv906823	chr16:69711533-69959223	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv1062171	chr16:69854267-70188585	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv542941	chr16:69854267-70188585	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
4	nsv1059249	chr16:69854467-70188446	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
5	nsv542942	chr16:69854467-70188446	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
6	esv2758428	chr16:69855122-70313222	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
7	esv2758652	chr16:69855122-70313222	Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
8	esv1792580	chr16:69950347-70005207	Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
9	esv1801278	chr16:69951043-70050770	Enhancers Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
10	esv1829103	chr16:69951043-70050770	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2270838	HPR	cis	cerebellum	SCAN
rs2270838	DDX19A	cis	cerebellum	SCAN
rs2270838	WWP2	cis	cerebellum	SCAN
rs2270838	LOC440348	Cis_chr	lymphoblastoid	RTeQTL
rs2270838	PDPR	cis	parietal	SCAN
rs2270838	LOC283970	cis	multi-tissue	Pritchard
rs2270838	LOC440348	cis	multi-tissue	Pritchard

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:69911400-69970200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr16:69924400-69965000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr16:69939000-69974000	Weak transcription	Fetal Brain Male	brain
4	chr16:69939600-69967600	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr16:69943200-69965600	Weak transcription	Brain Germinal Matrix	brain
6	chr16:69943400-69959400	Weak transcription	Pancreas	Pancrea
7	chr16:69943600-69965000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr16:69943600-69967000	Weak transcription	Small Intestine	intestine
9	chr16:69944000-69959600	Weak transcription	Fetal Thymus	thymus
10	chr16:69945200-69964600	Weak transcription	Primary hematopoietic stem cells	blood
11	chr16:69945400-69964000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr16:69945600-69969400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr16:69947600-69977200	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr16:69948200-69977400	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr16:69948400-69977400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr16:69952200-69959800	Weak transcription	GM12878-XiMat	blood
17	chr16:69952200-69961000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr16:69952200-69965000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr16:69952400-69963800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr16:69952600-69959400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr16:69952600-69959400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr16:69952600-69959400	Weak transcription	Spleen	Spleen
23	chr16:69952600-69963600	Weak transcription	NHEK	skin
24	chr16:69952600-69976000	Weak transcription	Hela-S3	cervix
25	chr16:69952800-69963200	Weak transcription	Fetal Brain Female	brain
26	chr16:69952800-69965000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr16:69952800-69966800	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr16:69953600-69974800	Weak transcription	A549	lung
29	chr16:69954000-69961200	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr16:69954400-69976000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr16:69954600-69959600	Weak transcription	Primary B cells from cord blood	blood
32	chr16:69955600-69959400	Weak transcription	Liver	Liver
33	chr16:69955600-69959400	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr16:69955600-69961200	Weak transcription	Psoas Muscle	Psoas
35	chr16:69955800-69959400	Weak transcription	Gastric	stomach
36	chr16:69955800-69960400	Weak transcription	Brain Cingulate Gyrus	brain
37	chr16:69956400-69975600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr16:69957400-69959600	Enhancers	ES-I3 Cell Line	embryonic stem cell
39	chr16:69957400-69959800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr16:69957400-69961000	Strong transcription	Primary T helper cells PMA-I stimulated	--
41	chr16:69957400-69964400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
42	chr16:69957400-69977400	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr16:69957600-69975400	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr16:69957800-69959800	Enhancers	HepG2	liver
45	chr16:69957800-69960000	Enhancers	Fetal Muscle Trunk	muscle
46	chr16:69957800-69960200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr16:69957800-69962200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr16:69957800-69977200	Strong transcription	Fetal Intestine Small	intestine
49	chr16:69958000-69959400	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr16:69958000-69959600	Enhancers	HSMM	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links