Variant report

Variant	rs4625053
Chromosome Location	chr8:19317270-19317271
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:19316428..19318779-chr8:19615686..19617194,2	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10888163	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12155539	1.00[ASN][1000 genomes]
rs12680768	0.95[ASN][1000 genomes]
rs13261824	1.00[ASN][1000 genomes]
rs34221121	0.96[ASN][1000 genomes]
rs35736969	0.96[ASN][1000 genomes]
rs4072131	0.86[ASN][1000 genomes]
rs4379462	0.88[ASN][1000 genomes]
rs4391455	0.84[ASN][1000 genomes]
rs4409408	0.88[ASN][1000 genomes]
rs4427190	0.93[ASN][1000 genomes]
rs4442162	0.84[ASN][1000 genomes]
rs4486225	1.00[ASN][1000 genomes]
rs4922030	0.86[ASN][1000 genomes]
rs56298301	0.86[EUR][1000 genomes]
rs58551730	1.00[ASN][1000 genomes]
rs62496184	0.87[ASN][1000 genomes]
rs6586834	0.81[ASN][1000 genomes]
rs7002357	0.80[ASN][1000 genomes]
rs7011587	0.86[ASN][1000 genomes]
rs7828025	1.00[ASN][1000 genomes]
rs7836239	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015395	chr8:18489538-19370258	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv429907	chr8:18578720-19398220	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv949745	chr8:18826830-19363963	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv1016482	chr8:18834807-19339487	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv533109	chr8:18845845-19456780	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv949636	chr8:18957705-19664732	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv948861	chr8:19199688-19609029	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv949304	chr8:19199688-19625912	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
9	esv3693374	chr8:19241970-19359184	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
10	esv34007	chr8:19252602-19482098	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
11	nsv1022344	chr8:19270143-19324083	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
12	nsv890623	chr8:19307051-19383697	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs4625053	CSGALNACT1	cis	brain	BrainEAC
rs4625053	CSGALNACT1	cis	intralobular white matter	BrainEAC
rs4625053	CSGALNACT1	cis	inferior olivary nucleus	BrainEAC
rs4625053	CSGALNACT1	cis	Thyroid	GTEx
rs4625053	CSGALNACT1	cis	occipital cortex	BrainEAC
rs4625053	CSGALNACT1	cis	frontal cortex	BrainEAC
rs4625053	CSGALNACT1	cis	hippocampus	BrainEAC
rs4625053	CSGALNACT1	cis	putamen	BrainEAC
rs4625053	CSGALNACT1	cis	substantia nigra	BrainEAC
rs4625053	CSGALNACT1	cis	temporal cortex	BrainEAC
rs4625053	CSGALNACT1	cis	Skin Sun Exposed Lower leg	GTEx
rs4625053	CSGALNACT1	cis	Nerve Tibial	GTEx
rs4625053	CSGALNACT1	cis	thalamus	BrainEAC

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:19295000-19318800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr8:19296600-19317400	Weak transcription	Hela-S3	cervix
3	chr8:19297600-19319000	Weak transcription	Spleen	Spleen
4	chr8:19300600-19319200	Weak transcription	Gastric	stomach
5	chr8:19302800-19317800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr8:19305600-19317600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr8:19305600-19318400	Weak transcription	Pancreas	Pancrea
8	chr8:19306800-19322400	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr8:19308200-19317400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr8:19308200-19319000	Weak transcription	Lung	lung
11	chr8:19308400-19318200	Weak transcription	Right Ventricle	heart
12	chr8:19309800-19318400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr8:19310400-19317400	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr8:19310400-19317600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr8:19310600-19359600	Weak transcription	Ovary	ovary
16	chr8:19310800-19317400	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr8:19311200-19318000	Weak transcription	Primary hematopoietic stem cells	blood
18	chr8:19311400-19319400	Weak transcription	Thymus	Thymus
19	chr8:19313400-19327200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr8:19313800-19317400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr8:19313800-19318000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr8:19314000-19317400	Enhancers	Primary T cells from cord blood	blood
23	chr8:19314000-19318400	Weak transcription	Left Ventricle	heart
24	chr8:19314200-19319000	Weak transcription	Right Atrium	heart
25	chr8:19314600-19317800	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr8:19314600-19318000	Weak transcription	Brain Angular Gyrus	brain
27	chr8:19314800-19322400	Enhancers	Fetal Thymus	thymus
28	chr8:19315600-19317600	Weak transcription	Aorta	Aorta
29	chr8:19315800-19317800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr8:19315800-19321400	Weak transcription	Adipose Nuclei	Adipose
31	chr8:19316000-19317400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr8:19316000-19318000	Weak transcription	Placenta	Placenta
33	chr8:19316000-19318200	Weak transcription	Brain Hippocampus Middle	brain
34	chr8:19316000-19318600	Enhancers	HepG2	liver
35	chr8:19316200-19318200	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr8:19316200-19318400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr8:19316200-19318400	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr8:19316200-19319000	Weak transcription	Fetal Stomach	stomach
39	chr8:19316200-19319400	Weak transcription	Primary B cells from cord blood	blood
40	chr8:19316200-19339200	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr8:19316400-19317400	Enhancers	Primary T killer memory cells from peripheral blood	blood
42	chr8:19316400-19317800	Weak transcription	Fetal Brain Female	brain
43	chr8:19316400-19322200	Enhancers	Primary T cells fromperipheralblood	blood
44	chr8:19316400-19323800	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr8:19316600-19319400	Enhancers	Fetal Muscle Leg	muscle
46	chr8:19316800-19319000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
47	chr8:19317000-19317400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
48	chr8:19317000-19317400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
49	chr8:19317000-19317600	Enhancers	HUVEC	blood vessel
50	chr8:19317000-19318000	Weak transcription	Fetal Brain Male	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links