Variant report

Variant	rs10868
Chromosome Location	chr9:110092856-110092857
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:110043423..110046369-chr9:110091728..110093276,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000119318	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11573607	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11573662	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11573665	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11573703	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11573709	1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[ASN][1000 genomes]
rs11573711	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11573721	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12379885	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12379895	1.00[ASN][1000 genomes]
rs13287251	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1805331	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34593991	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34731486	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34745099	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35218924	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35494237	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35626978	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35827173	1.00[ASN][1000 genomes]
rs35865856	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35967129	1.00[ASN][1000 genomes]
rs36016101	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36089467	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56161943	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs66495692	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66539130	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67630898	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71495992	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs716004	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869351	chr9:109593212-110191170	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv530948	chr9:109760752-110413602	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10868	ENSG00000119318	cis	multi-tissue	Pritchard
rs10868	RAD23B	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:110058600-110098600	Weak transcription	Small Intestine	intestine
2	chr9:110061400-110094600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr9:110065600-110098600	Strong transcription	Dnd41	blood
4	chr9:110070200-110104400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr9:110070400-110099400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr9:110071400-110103000	Weak transcription	Stomach Mucosa	stomach
7	chr9:110075200-110093400	Weak transcription	Esophagus	oesophagus
8	chr9:110077600-110093800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr9:110079400-110097400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr9:110079600-110095800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr9:110079600-110098800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr9:110079800-110094600	Weak transcription	Brain Angular Gyrus	brain
13	chr9:110079800-110097600	Strong transcription	HSMM	muscle
14	chr9:110079800-110098000	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr9:110080000-110096800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr9:110080200-110097200	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr9:110080600-110097000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr9:110080600-110097400	Strong transcription	Primary B cells from cord blood	blood
19	chr9:110080600-110097800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr9:110084000-110096600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr9:110084000-110097800	Strong transcription	Hela-S3	cervix
22	chr9:110084800-110098800	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr9:110085200-110094800	Weak transcription	Aorta	Aorta
24	chr9:110085400-110094600	Weak transcription	Brain Hippocampus Middle	brain
25	chr9:110085400-110097800	Strong transcription	Liver	Liver
26	chr9:110086200-110097200	Strong transcription	HepG2	liver
27	chr9:110086200-110097600	Strong transcription	NHLF	lung
28	chr9:110087000-110093200	ZNF genes & repeats	A549	lung
29	chr9:110087200-110093800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr9:110087200-110094600	Weak transcription	Colon Smooth Muscle	Colon
31	chr9:110087200-110098600	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr9:110087400-110093000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr9:110087400-110094600	Weak transcription	Colonic Mucosa	Colon
34	chr9:110087400-110095000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr9:110087400-110097200	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr9:110087600-110103400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr9:110088200-110096600	Strong transcription	NHDF-Ad	bronchial
38	chr9:110088400-110093400	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr9:110088400-110093800	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr9:110088400-110094800	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr9:110088400-110094800	Weak transcription	Brain Substantia Nigra	brain
42	chr9:110088400-110097200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr9:110088400-110097800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr9:110088400-110097800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr9:110088400-110098800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr9:110088400-110101400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr9:110088600-110093000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr9:110088600-110093400	Weak transcription	Stomach Smooth Muscle	stomach
49	chr9:110088600-110093600	Weak transcription	Ovary	ovary
50	chr9:110088600-110094000	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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