Variant report

Variant	rs7754843
Chromosome Location	chr6:161589477-161589478
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:161574755..161576557-chr6:161587307..161589686,2	K562	blood:
2	chr6:161495917..161498579-chr6:161589322..161591703,2	K562	blood:
3	chr6:161588147..161591123-chr6:161695063..161696658,2	K562	blood:
4	chr6:161588978..161591951-chr6:161662641..161667563,4	K562	blood:
5	chr6:161586766..161590077-chr6:161636291..161640021,3	K562	blood:
6	chr6:161560244..161562389-chr6:161588061..161590978,2	K562	blood:
7	chr6:161573780..161576255-chr6:161588186..161590338,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000026652	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1001422	0.85[CHD][hapmap]
rs1474914	1.00[ASN][1000 genomes]
rs16892229	0.81[ASN][1000 genomes]
rs1967716	1.00[ASN][1000 genomes]
rs2018762	0.81[ASN][1000 genomes]
rs2064718	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2314375	0.81[ASN][1000 genomes]
rs3798920	0.81[ASN][1000 genomes]
rs3798921	1.00[ASN][1000 genomes]
rs3798923	1.00[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3798924	0.86[CEU][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61552758	0.81[ASN][1000 genomes]
rs6924597	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6934457	1.00[CHD][hapmap];0.86[GIH][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap];1.00[ASN][1000 genomes]
rs73786014	0.81[ASN][1000 genomes]
rs7775897	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs940520	0.81[ASN][1000 genomes]
rs9456637	1.00[ASN][1000 genomes]
rs9458141	0.85[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv886817	chr6:161371621-161846654	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	esv3381361	chr6:161373617-161864101	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7754843	AGPAT4	cis	cerebellum	SCAN
rs7754843	SYTL3	cis	parietal	SCAN
rs7754843	LPAL2	cis	parietal	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:161544600-161589600	Weak transcription	Fetal Brain Male	brain
2	chr6:161548400-161590800	Weak transcription	Fetal Thymus	thymus
3	chr6:161554000-161591000	Weak transcription	Colonic Mucosa	Colon
4	chr6:161574600-161592400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr6:161575600-161591000	Weak transcription	Gastric	stomach
6	chr6:161575600-161593400	Weak transcription	Esophagus	oesophagus
7	chr6:161579200-161590200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr6:161580600-161590800	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr6:161582600-161591000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr6:161583800-161590800	Weak transcription	Rectal Smooth Muscle	rectum
11	chr6:161584200-161589600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr6:161584200-161589600	Weak transcription	Primary B cells from peripheral blood	blood
13	chr6:161584200-161589600	Weak transcription	HSMMtube	muscle
14	chr6:161584200-161591200	Weak transcription	Thymus	Thymus
15	chr6:161584200-161591800	Weak transcription	Right Ventricle	heart
16	chr6:161584800-161589600	Weak transcription	Liver	Liver
17	chr6:161584800-161591200	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr6:161585000-161589600	Weak transcription	Fetal Heart	heart
19	chr6:161585000-161591600	Weak transcription	Fetal Intestine Small	intestine
20	chr6:161585600-161591200	Weak transcription	Ovary	ovary
21	chr6:161585600-161626000	Weak transcription	Right Atrium	heart
22	chr6:161586400-161591000	Weak transcription	Fetal Kidney	kidney
23	chr6:161586600-161590000	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr6:161586600-161591000	Weak transcription	Lung	lung
25	chr6:161586800-161591200	Weak transcription	Primary hematopoietic stem cells	blood
26	chr6:161587000-161592200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr6:161587200-161589800	Weak transcription	Primary B cells from cord blood	blood
28	chr6:161587200-161590600	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr6:161587400-161590600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr6:161587400-161592000	Enhancers	H1 Cell Line	embryonic stem cell
31	chr6:161587400-161599600	Weak transcription	Spleen	Spleen
32	chr6:161587400-161607000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr6:161587600-161589600	Weak transcription	Fetal Stomach	stomach
34	chr6:161587600-161589800	Weak transcription	Brain Germinal Matrix	brain
35	chr6:161587600-161590200	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr6:161587600-161590400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr6:161587600-161590400	Enhancers	iPS-18 Cell Line	embryonic stem cell
38	chr6:161587600-161590400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr6:161587600-161590800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr6:161587600-161591200	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr6:161587600-161592200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr6:161587600-161594000	Weak transcription	Aorta	Aorta
43	chr6:161587800-161590000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
44	chr6:161587800-161590800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr6:161587800-161592000	Enhancers	Cortex derived primary cultured neurospheres	brain
46	chr6:161587800-161592200	Enhancers	Brain Hippocampus Middle	brain
47	chr6:161587800-161592400	Enhancers	iPS-20b Cell Line	embryonic stem cell
48	chr6:161588000-161590000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr6:161588000-161599800	Weak transcription	Primary T cells from cord blood	blood
50	chr6:161588200-161591600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links