Variant report

Variant	rs926674
Chromosome Location	chr6:39019503-39019504
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:39014216..39015762-chr6:39017423..39020213,2	K562	blood:

Extended variants
information (count: 18 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1018420	1.00[CHB][hapmap]
rs1033524	1.00[CHB][hapmap]
rs12200524	1.00[JPT][hapmap]
rs12660306	1.00[AFR][1000 genomes]
rs1537231	1.00[ASW][hapmap]
rs1929899	1.00[JPT][hapmap]
rs2395710	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4714203	0.85[MEX][hapmap]
rs506672	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs9470961	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1028088	chr6:38821047-39163549	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers 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 miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv538205	chr6:38821047-39163549	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv885821	chr6:38843970-39039503	Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv948357	chr6:38920998-39035836	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1027064	chr6:38984374-39034516	Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	esv1801734	chr6:38986164-39034484	Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv528286	chr6:39019503-39060478	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs926674	NDUFB8	trans	parietal	SCAN
rs926674	CCNA1	trans	lymphoblastoid	seeQTL
rs926674	PI16	cis	cerebellum	SCAN
rs926674	MED20	cis	parietal	SCAN
rs926674	MRPL2	cis	parietal	SCAN
rs926674	TREM1	cis	parietal	SCAN
rs926674	LHFPL5	cis	cerebellum	SCAN
rs926674	GALNT9	trans	lymphoblastoid	seeQTL
rs926674	USP49	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:39016000-39020000	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr6:39017200-39030200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:39017400-39019800	Flanking Active TSS	Fetal Heart	heart
4	chr6:39017400-39020200	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr6:39017800-39020400	Enhancers	HMEC	breast
6	chr6:39017800-39020600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr6:39017800-39021000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr6:39017800-39026400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr6:39018200-39020000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr6:39018400-39019600	Enhancers	NHEK	skin
11	chr6:39018800-39020000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr6:39018800-39020000	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr6:39018800-39020000	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr6:39018800-39020400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr6:39018800-39023400	Enhancers	Pancreas	Pancrea
16	chr6:39019000-39019600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr6:39019000-39021400	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr6:39019200-39019600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr6:39019200-39019600	Enhancers	Primary hematopoietic stem cells	blood
20	chr6:39019200-39019600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr6:39019200-39019600	Enhancers	Right Atrium	heart
22	chr6:39019200-39019800	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr6:39019200-39019800	Enhancers	Primary T killer memory cells from peripheral blood	blood
24	chr6:39019200-39019800	Enhancers	Lung	lung
25	chr6:39019200-39019800	Enhancers	Right Ventricle	heart
26	chr6:39019200-39020000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
27	chr6:39019200-39020000	Flanking Active TSS	Dnd41	blood
28	chr6:39019200-39020000	Enhancers	GM12878-XiMat	blood
29	chr6:39019200-39020200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr6:39019200-39020200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr6:39019400-39019600	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr6:39019400-39019600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr6:39019400-39019800	Enhancers	Primary T helper naive cells from peripheral blood	blood
34	chr6:39019400-39019800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
35	chr6:39019400-39022200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr6:39019400-39022200	Weak transcription	Left Ventricle	heart

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