Variant report

Variant	rs8729
Chromosome Location	chr9:21331119-21331120
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:21325580..21327702-chr9:21329735..21331651,2	MCF-7	breast:
2	chr9:21328009..21333190-chr9:21333474..21336678,6	MCF-7	breast:
3	chr9:21326879..21332228-chr9:21332519..21336640,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198642	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10116615	0.94[EUR][1000 genomes]
rs10117677	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10119678	1.00[ASW][hapmap];0.82[CEU][hapmap];0.87[MEX][hapmap];0.92[YRI][hapmap]
rs10125010	0.94[CEU][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap]
rs10738591	0.91[CHB][hapmap]
rs10757212	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10757213	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10811505	0.94[CEU][hapmap]
rs10811522	1.00[CEU][hapmap];0.91[CHB][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10811523	1.00[CEU][hapmap];0.85[CHB][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10964878	0.83[MEX][hapmap]
rs10964953	1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10964954	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10964955	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10964956	1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10964958	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10964960	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10964966	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12237982	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1224392	0.91[EUR][1000 genomes]
rs12553910	0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12683349	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1330311	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1330313	1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1330314	0.80[ASW][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap]
rs1360286	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1411437	0.85[EUR][1000 genomes]
rs1467734	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1467735	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1467736	1.00[CEU][hapmap];0.91[CHB][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1475547	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1475548	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1543874	1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1820314	0.89[CEU][hapmap]
rs1831390	0.85[EUR][1000 genomes]
rs2094787	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2094788	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2480927	0.91[EUR][1000 genomes]
rs3758236	0.91[CHB][hapmap]
rs4406500	0.95[EUR][1000 genomes]
rs4978056	0.85[EUR][1000 genomes]
rs4978092	0.95[EUR][1000 genomes]
rs4978093	0.94[EUR][1000 genomes]
rs4978097	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs57371737	0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs600118	0.97[EUR][1000 genomes]
rs616873	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6475527	0.91[EUR][1000 genomes]
rs667069	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs67212517	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7020867	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7021699	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7031048	0.91[CHB][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap]
rs7032044	0.93[EUR][1000 genomes]
rs7035600	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7035669	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7849623	0.87[MEX][hapmap]
rs7849902	0.92[EUR][1000 genomes]
rs7853081	0.99[EUR][1000 genomes]
rs7862940	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7868334	0.94[CEU][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap]
rs7872479	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9298814	0.94[CEU][hapmap]

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	nsv892724	chr9:20690244-21517302	Genic enhancers Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription 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 miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases
2	nsv892736	chr9:21327141-21391698	Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs8729	KLHL9	cis	lymphoblastoid	seeQTL
rs8729	ENSG00000198642	cis	multi-tissue	Pritchard
rs8729	KLHL9	cis	multi-tissue	Pritchard

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21317200-21331600	Weak transcription	Esophagus	oesophagus
2	chr9:21317200-21331600	Weak transcription	Gastric	stomach
3	chr9:21318800-21331200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr9:21318800-21331800	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr9:21318800-21332600	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr9:21318800-21332800	Weak transcription	Fetal Kidney	kidney
7	chr9:21319000-21332200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr9:21319000-21333200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr9:21319600-21333200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr9:21320600-21331600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr9:21321400-21331600	Weak transcription	Spleen	Spleen
12	chr9:21321600-21333400	Weak transcription	Colonic Mucosa	Colon
13	chr9:21322000-21331600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr9:21322000-21331600	Weak transcription	HepG2	liver
15	chr9:21322200-21333600	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr9:21323400-21331800	Weak transcription	Aorta	Aorta
17	chr9:21323400-21333800	Weak transcription	Lung	lung
18	chr9:21323600-21331600	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr9:21323800-21331800	Weak transcription	Stomach Smooth Muscle	stomach
20	chr9:21324000-21331400	Weak transcription	Right Ventricle	heart
21	chr9:21324000-21333000	Weak transcription	Placenta	Placenta
22	chr9:21324200-21331600	Weak transcription	Fetal Thymus	thymus
23	chr9:21324200-21331600	Weak transcription	A549	lung
24	chr9:21324400-21331600	Weak transcription	Thymus	Thymus
25	chr9:21324400-21333200	Weak transcription	Primary B cells from cord blood	blood
26	chr9:21324400-21333200	Weak transcription	Fetal Stomach	stomach
27	chr9:21324400-21333400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr9:21324800-21331400	Weak transcription	NHLF	lung
29	chr9:21324800-21331600	Weak transcription	Primary B cells from peripheral blood	blood
30	chr9:21324800-21331600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr9:21324800-21333000	Weak transcription	Fetal Intestine Large	intestine
32	chr9:21324800-21333000	Weak transcription	Fetal Muscle Trunk	muscle
33	chr9:21324800-21333000	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr9:21324800-21333200	Weak transcription	Primary hematopoietic stem cells	blood
35	chr9:21325000-21331600	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr9:21325000-21333000	Weak transcription	Fetal Intestine Small	intestine
37	chr9:21325200-21331600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr9:21325200-21331600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr9:21326200-21333000	Weak transcription	HSMMtube	muscle
40	chr9:21326800-21333000	Enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr9:21326800-21333200	Enhancers	Colon Smooth Muscle	Colon
42	chr9:21326800-21333400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr9:21326800-21333600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
44	chr9:21326800-21333800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
45	chr9:21327000-21331600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
46	chr9:21327000-21331600	Weak transcription	Brain Cingulate Gyrus	brain
47	chr9:21327200-21331600	Weak transcription	Hela-S3	cervix
48	chr9:21327600-21331600	Genic enhancers	Dnd41	blood
49	chr9:21328400-21331600	Weak transcription	Brain Angular Gyrus	brain
50	chr9:21328600-21331400	Weak transcription	Fetal Brain Male	brain

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