Variant report

Variant	rs1193288
Chromosome Location	chr8:19145800-19145801
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	chr8:19144461..19147739-chr8:19170304..19172981,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000104611	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10088667	0.81[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs10091480	0.81[CHB][hapmap];0.89[JPT][hapmap]
rs10091481	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs10092550	0.81[CHB][hapmap];0.89[JPT][hapmap]
rs10105631	0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs10108694	0.82[ASN][1000 genomes]
rs11204027	0.83[ASN][1000 genomes]
rs11779774	0.82[ASN][1000 genomes]
rs1193284	0.81[CHB][hapmap];0.81[ASN][1000 genomes]
rs1193287	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1193289	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1193290	0.81[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs1193291	0.88[ASN][1000 genomes]
rs1193292	0.81[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs1193293	0.87[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1193294	0.81[CHB][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs1193296	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1193297	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1193304	0.81[EUR][1000 genomes]
rs1193305	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1193308	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1193309	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1193329	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13261970	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1473939	0.82[ASN][1000 genomes]
rs1473940	0.81[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs1514701	0.81[EUR][1000 genomes]
rs1514702	0.81[ASN][1000 genomes]
rs1915406	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1915407	0.81[ASN][1000 genomes]
rs2244976	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2249278	0.89[JPT][hapmap]
rs2672225	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2672226	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2672227	0.86[EUR][1000 genomes]
rs2672254	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2672260	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2672262	0.90[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2672264	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2683280	0.81[CHB][hapmap];0.89[JPT][hapmap]
rs2683285	0.82[ASN][1000 genomes]
rs2683312	0.81[AMR][1000 genomes]
rs2683313	0.86[CEU][hapmap];0.89[JPT][hapmap];0.87[EUR][1000 genomes]
rs2683314	0.90[CEU][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2683316	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2943422	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2943426	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2943430	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2947260	0.81[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.81[TSI][hapmap]
rs2947261	0.97[GIH][hapmap];0.84[JPT][hapmap];0.81[TSI][hapmap]
rs2947262	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34192188	0.81[ASN][1000 genomes]
rs4922006	0.81[ASN][1000 genomes]
rs4922007	0.81[ASN][1000 genomes]
rs55846624	0.85[ASN][1000 genomes]
rs6586820	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6586822	0.81[ASN][1000 genomes]
rs6586823	0.82[ASN][1000 genomes]
rs7814080	0.81[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs7841513	0.83[ASN][1000 genomes]
rs991589	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026466	chr8:18433493-19271274	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv539520	chr8:18433493-19271274	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	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
4	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
5	nsv917232	chr8:18585309-19208665	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	nsv890610	chr8:18749120-19260599	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	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
8	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
9	nsv890614	chr8:18838764-19274793	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
10	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
11	nsv1016993	chr8:18855623-19311731	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
12	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
13	nsv890615	chr8:18989735-19181921	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
14	nsv890616	chr8:18989735-19197809	Weak transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
15	nsv1033229	chr8:19081684-19271274	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
16	nsv1033297	chr8:19108472-19150023	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
17	nsv1034119	chr8:19115084-19164833	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
18	nsv465599	chr8:19115136-19159082	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
19	nsv610747	chr8:19115136-19159082	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
20	nsv465600	chr8:19116030-19156100	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
21	nsv610748	chr8:19116030-19156100	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
22	nsv610749	chr8:19116030-19160915	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
23	nsv470202	chr8:19128303-19168142	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
24	nsv610750	chr8:19128303-19168142	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1193288	CSGALNACT1	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:19138400-19148800	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr8:19140400-19146000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr8:19145000-19147200	Weak transcription	Placenta	Placenta
4	chr8:19145000-19148400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr8:19145000-19149800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr8:19145400-19151200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr8:19145600-19147200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr8:19145600-19147200	Enhancers	HMEC	breast
9	chr8:19145600-19147200	Enhancers	NHEK	skin
10	chr8:19145600-19147600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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