Variant report

Variant	rs9646522
Chromosome Location	chr18:45691715-45691716
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	EP300	chr18:45691714-45692107	HepG2	liver:	n/a	n/a
2	MYC	chr18:45691714-45692313	NB4	blood:	n/a	n/a
3	POLR2A	chr18:45691691-45691990	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
ZBTB7C	TF binding region

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11663174	0.91[ASN][1000 genomes]
rs12454335	0.90[ASN][1000 genomes]
rs12606239	0.81[ASN][1000 genomes]
rs34962603	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4258692	0.87[EUR][1000 genomes]
rs4281790	0.88[ASN][1000 genomes]
rs55707477	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62087433	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62087434	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7236506	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8092444	0.81[CHB][hapmap]
rs9789091	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9953128	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9967534	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv909616	chr18:45467806-45844500	Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9646522	LIPG	cis	cerebellum	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:45688400-45699200	Enhancers	Spleen	Spleen
2	chr18:45688600-45692400	Enhancers	Fetal Kidney	kidney
3	chr18:45688600-45693200	Weak transcription	Psoas Muscle	Psoas
4	chr18:45688800-45692000	Enhancers	Fetal Stomach	stomach
5	chr18:45688800-45692200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr18:45688800-45692200	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr18:45688800-45692800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr18:45688800-45692800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr18:45688800-45693000	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr18:45688800-45693200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr18:45688800-45693200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr18:45688800-45693200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr18:45688800-45693400	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr18:45688800-45694800	Enhancers	Fetal Muscle Leg	muscle
15	chr18:45688800-45695600	Enhancers	Placenta	Placenta
16	chr18:45688800-45696600	Enhancers	Fetal Intestine Small	intestine
17	chr18:45688800-45696800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr18:45688800-45697000	Enhancers	Fetal Intestine Large	intestine
19	chr18:45688800-45697000	Enhancers	Ovary	ovary
20	chr18:45689000-45692400	Enhancers	Rectal Mucosa Donor 29	rectum
21	chr18:45689000-45692600	Enhancers	Fetal Lung	lung
22	chr18:45689000-45693000	Weak transcription	Stomach Smooth Muscle	stomach
23	chr18:45689000-45693200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr18:45689000-45693600	Enhancers	Stomach Mucosa	stomach
25	chr18:45689000-45693800	Weak transcription	Brain Hippocampus Middle	brain
26	chr18:45689200-45695800	Enhancers	Duodenum Mucosa	Duodenum
27	chr18:45689400-45693200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr18:45689800-45693200	Weak transcription	Brain Cingulate Gyrus	brain
29	chr18:45689800-45693200	Weak transcription	Brain Substantia Nigra	brain
30	chr18:45690000-45691800	Weak transcription	Gastric	stomach
31	chr18:45690200-45692800	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr18:45690200-45695800	Enhancers	Hela-S3	cervix
33	chr18:45690400-45692800	Weak transcription	Right Ventricle	heart
34	chr18:45690800-45692200	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr18:45690800-45692400	Enhancers	Sigmoid Colon	Sigmoid Colon
36	chr18:45690800-45693000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr18:45691000-45692000	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
38	chr18:45691000-45692200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
39	chr18:45691000-45692400	Enhancers	Small Intestine	intestine
40	chr18:45691200-45693200	Enhancers	Adipose Nuclei	Adipose
41	chr18:45691200-45694000	Enhancers	Primary B cells from cord blood	blood
42	chr18:45691200-45694200	Enhancers	Primary hematopoietic stem cells	blood
43	chr18:45691200-45694200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr18:45691200-45694600	Enhancers	Primary monocytes fromperipheralblood	blood
45	chr18:45691400-45691800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
46	chr18:45691400-45692400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
47	chr18:45691400-45694000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr18:45691400-45694600	Enhancers	Fetal Muscle Trunk	muscle
49	chr18:45691400-45694600	Enhancers	Right Atrium	heart
50	chr18:45691600-45691800	Enhancers	H1 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links