Variant report

Variant	rs332841
Chromosome Location	chr19:38674691-38674692
allele	C/T
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	SIN3A	chr19:38673863-38674695	H1-hESC	embryonic stem cell:	n/a	n/a
2	RAD21	chr19:38674287-38674718	H1-hESC	embryonic stem cell:	n/a	n/a
3	TBP	chr19:38674132-38674695	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:38673271..38675565-chr19:38714868..38716918,2	K562	blood:

Variant related genes	Relation type
ENSG00000269653	TF binding region
ENSG00000011332	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10414253	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12985707	0.88[CEU][hapmap]
rs2010234	0.88[CEU][hapmap]
rs2304132	0.88[CEU][hapmap];0.81[GIH][hapmap]
rs2569413	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs332852	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs332853	0.85[AMR][1000 genomes]
rs332854	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs332857	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs332863	0.92[CEU][hapmap];0.81[GIH][hapmap]
rs3852911	0.84[CEU][hapmap]
rs62123462	0.89[EUR][1000 genomes]
rs7253312	0.88[CEU][hapmap]
rs7253633	0.88[CEU][hapmap]
rs8107385	0.88[CEU][hapmap];0.81[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv833821	chr19:38629937-38756792	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv911657	chr19:38655449-38753786	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs332841	EGLN2	cis	cerebellum	SCAN
rs332841	ERCC2	cis	cerebellum	SCAN
rs332841	ERF	cis	cerebellum	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38653600-38696400	Weak transcription	Small Intestine	intestine
2	chr19:38656200-38675200	Weak transcription	Stomach Mucosa	stomach
3	chr19:38657600-38696200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr19:38658400-38684800	Weak transcription	HepG2	liver
5	chr19:38658400-38694000	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr19:38661400-38682600	Weak transcription	Aorta	Aorta
7	chr19:38661800-38682400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr19:38664600-38688600	Weak transcription	NH-A	brain
9	chr19:38664600-38699800	Weak transcription	Brain Substantia Nigra	brain
10	chr19:38665000-38684400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr19:38665200-38684200	Weak transcription	HMEC	breast
12	chr19:38666200-38682800	Weak transcription	Right Ventricle	heart
13	chr19:38670800-38677400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr19:38671000-38676600	Strong transcription	Duodenum Mucosa	Duodenum
15	chr19:38671000-38676800	Strong transcription	Primary T cells from cord blood	blood
16	chr19:38671200-38676800	Strong transcription	Liver	Liver
17	chr19:38671200-38684400	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr19:38671200-38691800	Weak transcription	Brain Angular Gyrus	brain
19	chr19:38671800-38675400	Weak transcription	Dnd41	blood
20	chr19:38671800-38676800	Strong transcription	Primary B cells from cord blood	blood
21	chr19:38671800-38677200	Strong transcription	Primary B cells from peripheral blood	blood
22	chr19:38671800-38692400	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr19:38671800-38695600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr19:38672000-38675600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr19:38672000-38677800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr19:38672200-38675400	Weak transcription	Left Ventricle	heart
27	chr19:38672200-38692800	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr19:38672600-38676800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr19:38672600-38677000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr19:38672600-38699800	Weak transcription	HUVEC	blood vessel
31	chr19:38672800-38676800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr19:38672800-38693400	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr19:38673000-38676600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr19:38673000-38676800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr19:38673000-38676800	Strong transcription	A549	lung
36	chr19:38673200-38674800	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
37	chr19:38673200-38676400	Strong transcription	Lung	lung
38	chr19:38673200-38676800	Strong transcription	Gastric	stomach
39	chr19:38673200-38676800	Strong transcription	Spleen	Spleen
40	chr19:38673400-38674800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr19:38673400-38674800	Enhancers	Fetal Brain Male	brain
42	chr19:38673600-38674800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
43	chr19:38673600-38674800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
44	chr19:38673600-38674800	Flanking Active TSS	NHLF	lung
45	chr19:38673800-38674800	Flanking Active TSS	H1 Cell Line	embryonic stem cell
46	chr19:38673800-38674800	Flanking Active TSS	Brain Germinal Matrix	brain
47	chr19:38673800-38674800	Transcr. at gene 5' and 3'	Fetal Stomach	stomach
48	chr19:38673800-38674800	Weak transcription	GM12878-XiMat	blood
49	chr19:38673800-38675000	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr19:38673800-38675200	Weak transcription	Sigmoid Colon	Sigmoid Colon

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