Variant report

Variant	rs1620833
Chromosome Location	chr8:11734875-11734876
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:11727352..11730707-chr8:11734493..11737265,3	K562	blood:
2	chr8:11724112..11726454-chr8:11732632..11735297,3	K562	blood:
3	chr8:11710084..11711593-chr8:11733792..11735545,2	K562	blood:
4	chr8:11724798..11726931-chr8:11734409..11737375,2	K562	blood:
5	chr8:11724109..11726850-chr8:11734821..11736918,2	MCF-7	breast:
6	chr8:11734290..11736871-chr8:11743194..11744743,2	K562	blood:
7	chr8:11200722..11203684-chr8:11734586..11737466,2	K562	blood:

Variant related genes	Relation type
ENSG00000164733	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1293309	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1293310	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1293311	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1296023	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1619003	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1619200	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1624088	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1630950	0.83[ASN][1000 genomes]
rs1692791	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1692803	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1692804	0.86[ASN][1000 genomes]
rs1692807	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1692808	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1692809	0.83[ASN][1000 genomes]
rs1692810	0.81[ASN][1000 genomes]
rs1736117	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1736118	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1736119	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1736120	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1736121	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2250903	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2472430	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2645412	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2740596	0.89[ASN][1000 genomes]
rs2740597	0.89[ASN][1000 genomes]
rs2740600	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2740601	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2740602	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3104255	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3116070	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3116071	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7828791	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7844154	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs904016	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs904017	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs966785	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs966786	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs966787	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:27 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529399	chr8:10970091-11805960	Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv1018978	chr8:11438267-11858466	Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv917963	chr8:11540723-11751798	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1027378	chr8:11541739-11858466	Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv1028229	chr8:11575762-11805961	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv539475	chr8:11575762-11805961	Flanking Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv428514	chr8:11580381-11765706	Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
8	nsv1034014	chr8:11602337-11858466	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
9	nsv890361	chr8:11625808-11755513	Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
10	nsv890362	chr8:11625808-11771089	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
11	nsv1034132	chr8:11657033-12198242	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
12	nsv890365	chr8:11666451-11735641	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
13	nsv890366	chr8:11666451-11900847	Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
14	nsv1031158	chr8:11666558-11759064	Bivalent Enhancer Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
15	nsv539477	chr8:11666558-11759064	Enhancers Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
16	nsv1018042	chr8:11667496-11882385	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
17	nsv890367	chr8:11668153-11793529	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
18	nsv890369	chr8:11671041-11840011	Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
19	nsv1016952	chr8:11679271-11849955	Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
20	nsv1029093	chr8:11679271-11858466	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
21	nsv539478	chr8:11679271-11858466	Bivalent/Poised TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
22	nsv1031972	chr8:11696393-11805961	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
23	nsv539481	chr8:11696393-11805961	Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
24	nsv610293	chr8:11698747-11929734	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
25	nsv516685	chr8:11698747-12570199	Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	74 gene(s)	inside rSNPs	diseases
26	nsv1032736	chr8:11727357-11762693	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
27	nsv1029694	chr8:11727357-11858466	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1620833	CTSB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:11726400-11735200	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr8:11726400-11735200	Weak transcription	Right Ventricle	heart
3	chr8:11726600-11736400	Weak transcription	Spleen	Spleen
4	chr8:11727400-11737800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr8:11731200-11736400	Enhancers	HMEC	breast
6	chr8:11731200-11738200	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr8:11731600-11737800	Enhancers	Placenta	Placenta
8	chr8:11731800-11736200	Enhancers	HUVEC	blood vessel
9	chr8:11731800-11736800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr8:11732200-11735200	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr8:11732600-11735200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr8:11732600-11735400	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr8:11732600-11736600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr8:11732800-11735200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr8:11732800-11735200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr8:11732800-11737200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr8:11734000-11738000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr8:11734000-11738000	Enhancers	HepG2	liver
19	chr8:11734200-11735000	Enhancers	Lung	lung
20	chr8:11734200-11735200	Enhancers	Primary B cells from cord blood	blood
21	chr8:11734200-11735200	Enhancers	GM12878-XiMat	blood
22	chr8:11734200-11735200	Enhancers	Osteobl	bone
23	chr8:11734200-11735600	Enhancers	Primary B cells from peripheral blood	blood
24	chr8:11734200-11735800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr8:11734200-11735800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr8:11734200-11735800	Enhancers	NHLF	lung
27	chr8:11734200-11736000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr8:11734200-11736200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr8:11734200-11736200	Enhancers	NH-A	brain
30	chr8:11734200-11736600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr8:11734200-11736600	Enhancers	NHDF-Ad	bronchial
32	chr8:11734200-11737800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr8:11734400-11735000	Enhancers	Liver	Liver
34	chr8:11734400-11735200	Enhancers	Primary T helper cells PMA-I stimulated	--
35	chr8:11734400-11735200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
36	chr8:11734400-11735400	Enhancers	Primary T cells from cord blood	blood
37	chr8:11734400-11736200	Enhancers	Duodenum Mucosa	Duodenum
38	chr8:11734400-11736200	Enhancers	Hela-S3	cervix
39	chr8:11734400-11736600	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr8:11734400-11737800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr8:11734600-11735000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr8:11734600-11735000	Enhancers	Adipose Nuclei	Adipose
43	chr8:11734600-11735000	Flanking Active TSS	A549	lung
44	chr8:11734600-11735200	Enhancers	Primary hematopoietic stem cells	blood
45	chr8:11734600-11735200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr8:11734600-11735200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
47	chr8:11734600-11735200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr8:11734600-11735200	Enhancers	Dnd41	blood
49	chr8:11734600-11735200	Enhancers	K562	blood
50	chr8:11734600-11735400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links