Variant report

Variant	rs12155539
Chromosome Location	chr8:19316086-19316087
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:19265734..19267679-chr8:19315325..19317057,2	MCF-7	breast:

Extended variants
information (count: 47 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10888163	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11204045	0.88[JPT][hapmap]
rs12680768	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12682196	0.90[CHB][hapmap];0.95[YRI][hapmap]
rs13250181	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap]
rs13258090	0.81[MKK][hapmap]
rs13261732	1.00[CHB][hapmap];0.95[YRI][hapmap]
rs13261824	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[ASN][1000 genomes]
rs3185	0.90[CHB][hapmap]
rs34221121	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35736969	0.96[ASN][1000 genomes]
rs4072131	0.88[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4292704	1.00[CHB][hapmap]
rs4379462	1.00[CHB][hapmap];0.88[CHD][hapmap];0.81[YRI][hapmap];0.88[ASN][1000 genomes]
rs4391455	0.84[ASN][1000 genomes]
rs4409408	1.00[CHB][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs4427190	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4431609	0.85[MKK][hapmap]
rs4442162	0.84[ASN][1000 genomes]
rs4486225	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4625053	1.00[ASN][1000 genomes]
rs4922028	0.80[LWK][hapmap];0.89[MKK][hapmap]
rs4922030	0.88[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4922031	0.82[ASW][hapmap];0.83[GIH][hapmap];0.91[MKK][hapmap];0.95[YRI][hapmap]
rs4922036	1.00[CHB][hapmap]
rs58551730	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62496184	0.87[ASN][1000 genomes]
rs6586834	0.81[ASN][1000 genomes]
rs6981898	0.82[MKK][hapmap]
rs6984449	0.90[CHB][hapmap]
rs7002357	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs7011587	0.86[ASN][1000 genomes]
rs7821446	0.86[MEX][hapmap]
rs7828025	1.00[CHB][hapmap];1.00[JPT][hapmap];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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12155539	CSGALNACT1	cis	parietal	SCAN
rs12155539	VPS37A	cis	parietal	SCAN
rs12155539	CSGALNACT1	cis	Thyroid	GTEx
rs12155539	CSGALNACT1	cis	cerebellum	SCAN

Chromatin state (count:68 , 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	chr8:19301600-19317200	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr8:19302800-19317800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr8:19305600-19317600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr8:19305600-19318400	Weak transcription	Pancreas	Pancrea
9	chr8:19306800-19322400	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr8:19308200-19317000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr8:19308200-19317000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr8:19308200-19317400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr8:19308200-19319000	Weak transcription	Lung	lung
14	chr8:19308400-19317200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr8:19308400-19318200	Weak transcription	Right Ventricle	heart
16	chr8:19309800-19318400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr8:19310400-19317400	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr8:19310400-19317600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr8:19310600-19359600	Weak transcription	Ovary	ovary
20	chr8:19310800-19317400	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr8:19311200-19318000	Weak transcription	Primary hematopoietic stem cells	blood
22	chr8:19311400-19319400	Weak transcription	Thymus	Thymus
23	chr8:19311600-19316200	Enhancers	Fetal Stomach	stomach
24	chr8:19311600-19316400	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr8:19312400-19317200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
26	chr8:19312600-19317000	Enhancers	Fetal Brain Male	brain
27	chr8:19313000-19317200	Enhancers	Primary T helper naive cells from peripheral blood	blood
28	chr8:19313200-19316200	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr8:19313200-19316400	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr8:19313400-19317200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr8:19313400-19327200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr8:19313800-19317400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr8:19313800-19318000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr8:19314000-19316200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr8:19314000-19317400	Enhancers	Primary T cells from cord blood	blood
36	chr8:19314000-19318400	Weak transcription	Left Ventricle	heart
37	chr8:19314200-19316600	Weak transcription	Fetal Muscle Leg	muscle
38	chr8:19314200-19319000	Weak transcription	Right Atrium	heart
39	chr8:19314600-19317800	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr8:19314600-19318000	Weak transcription	Brain Angular Gyrus	brain
41	chr8:19314800-19316200	Strong transcription	A549	lung
42	chr8:19314800-19322400	Enhancers	Fetal Thymus	thymus
43	chr8:19315000-19316200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr8:19315000-19316200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr8:19315200-19316200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
46	chr8:19315200-19316400	Enhancers	Stomach Mucosa	stomach
47	chr8:19315200-19317200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr8:19315400-19316200	Strong transcription	Primary B cells from cord blood	blood
49	chr8:19315600-19316200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr8:19315600-19316200	Flanking Active TSS	HUVEC	blood vessel

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