Variant report

Variant	rs1465923
Chromosome Location	chr4:77136211-77136212
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:77136166-77136667	MCF-7	breast:	n/a	n/a
2	GATA1	chr4:77136098-77137279	PBDE	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:77135441..77137897-chr4:77152068..77153830,2	K562	blood:
2	chr4:77132958..77141575-chr4:77150872..77159587,22	MCF-7	breast:
3	chr4:77067778..77069460-chr4:77134577..77136401,2	K562	blood:
4	chr4:77066331..77070645-chr4:77133023..77136401,5	K562	blood:
5	chr4:77131893..77139465-chr4:77152630..77158664,14	MCF-7	breast:
6	chr4:77132690..77134987-chr4:77135558..77138954,3	K562	blood:

No data

Variant related genes	Relation type
FAM47E	TF binding region
SCARB2	TF binding region
ENSG00000138750	Chromatin interaction
ENSG00000138760	Chromatin interaction
ENSG00000189157	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10032423	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1372410	0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs1372411	0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs1542093	0.82[JPT][hapmap]
rs1542094	0.82[JPT][hapmap]
rs1542095	0.82[JPT][hapmap]
rs17001391	0.82[JPT][hapmap]
rs17001392	0.82[JPT][hapmap];1.00[MEX][hapmap]
rs17001393	0.82[JPT][hapmap]
rs17001395	0.82[JPT][hapmap]
rs17001396	0.82[JPT][hapmap];1.00[MEX][hapmap]
rs17001398	0.82[JPT][hapmap];1.00[MEX][hapmap]
rs17001551	0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs17001559	0.82[JPT][hapmap]
rs17001593	0.82[JPT][hapmap]
rs17001598	0.82[JPT][hapmap]
rs17001601	0.82[JPT][hapmap]
rs17001606	0.82[JPT][hapmap]
rs17001633	0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs3733255	0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs4282210	1.00[ASW][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4416503	0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs4639101	0.82[JPT][hapmap]
rs6856609	0.82[JPT][hapmap]
rs7436214	0.82[JPT][hapmap]
rs7682766	0.82[JPT][hapmap]
rs7685696	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs894250	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs920608	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[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	esv3436996	chr4:77132828-77137126	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1465923	HSPA2	trans	brain	seeQTL
rs1465923	FAM53B	trans	brain	seeQTL
rs1465923	DYSF	trans	brain	seeQTL
rs1465923	RNF130	trans	brain	seeQTL

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:77135200-77136400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr4:77135200-77136400	Flanking Active TSS	Duodenum Mucosa	Duodenum
3	chr4:77135200-77136400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
4	chr4:77135200-77136400	Flanking Active TSS	Dnd41	blood
5	chr4:77135200-77136600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
6	chr4:77135200-77137400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
7	chr4:77135400-77136400	Flanking Active TSS	Brain Cingulate Gyrus	brain
8	chr4:77135400-77136400	Flanking Active TSS	Brain Hippocampus Middle	brain
9	chr4:77135400-77136400	Flanking Active TSS	Fetal Lung	lung
10	chr4:77135600-77136400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr4:77135600-77136400	Enhancers	Small Intestine	intestine
12	chr4:77135600-77136400	Enhancers	Spleen	Spleen
13	chr4:77135600-77136600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr4:77135600-77136600	Enhancers	Gastric	stomach
15	chr4:77135600-77136600	Enhancers	Placenta Amnion	Placenta Amnion
16	chr4:77135600-77137400	Enhancers	Esophagus	oesophagus
17	chr4:77135600-77137400	Enhancers	Lung	lung
18	chr4:77135600-77138600	Weak transcription	Ovary	ovary
19	chr4:77135600-77138800	Enhancers	Placenta	Placenta
20	chr4:77135800-77136400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr4:77135800-77136400	Enhancers	Colon Smooth Muscle	Colon
22	chr4:77135800-77136400	Enhancers	Stomach Mucosa	stomach
23	chr4:77135800-77136400	Enhancers	Thymus	Thymus
24	chr4:77135800-77136600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr4:77135800-77136600	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr4:77135800-77136600	Enhancers	Primary B cells from peripheral blood	blood
27	chr4:77135800-77136600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
28	chr4:77135800-77136600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr4:77135800-77136600	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr4:77135800-77136600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr4:77135800-77136600	Enhancers	Adipose Nuclei	Adipose
32	chr4:77135800-77136600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr4:77135800-77136600	Enhancers	Fetal Stomach	stomach
34	chr4:77135800-77136600	Enhancers	Left Ventricle	heart
35	chr4:77135800-77136600	Enhancers	Right Ventricle	heart
36	chr4:77135800-77136800	Enhancers	Primary T helper naive cells from peripheral blood	blood
37	chr4:77135800-77136800	Enhancers	Fetal Intestine Small	intestine
38	chr4:77135800-77136800	Enhancers	K562	blood
39	chr4:77135800-77137000	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr4:77135800-77137000	Enhancers	Primary T killer memory cells from peripheral blood	blood
41	chr4:77135800-77137000	Weak transcription	Aorta	Aorta
42	chr4:77135800-77137200	Enhancers	Duodenum Smooth Muscle	Duodenum
43	chr4:77135800-77138200	Weak transcription	HSMMtube	muscle
44	chr4:77135800-77138600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr4:77135800-77139000	Enhancers	Sigmoid Colon	Sigmoid Colon
46	chr4:77135800-77139800	Weak transcription	Osteobl	bone
47	chr4:77135800-77140000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr4:77135800-77141000	Enhancers	Psoas Muscle	Psoas
49	chr4:77135800-77142200	Enhancers	Primary monocytes fromperipheralblood	blood
50	chr4:77135800-77147400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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