Variant report

Variant	rs10117202
Chromosome Location	chr9:21323089-21323090
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 125 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:123)

rs_ID	r²[population]
rs10116540	0.93[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes]
rs10116936	0.86[ASN][1000 genomes]
rs10120117	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10122881	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10124167	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10124609	0.80[EUR][1000 genomes]
rs10738591	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs10757199	0.93[CEU][hapmap]
rs10811497	0.93[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs10811508	0.82[EUR][1000 genomes]
rs10811509	0.83[EUR][1000 genomes]
rs10811514	0.87[EUR][1000 genomes]
rs10811527	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10811529	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10964871	0.93[CEU][hapmap]
rs10964878	0.93[CEU][hapmap];0.95[TSI][hapmap]
rs10964884	0.92[CEU][hapmap]
rs10964885	0.93[CEU][hapmap]
rs10964896	0.93[CEU][hapmap]
rs10964918	0.87[EUR][1000 genomes]
rs10964920	0.93[CEU][hapmap]
rs10964928	0.89[EUR][1000 genomes]
rs10964929	0.85[EUR][1000 genomes]
rs10964930	0.93[CEU][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes]
rs10964932	0.93[CEU][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes]
rs10964933	0.89[EUR][1000 genomes]
rs10964934	0.93[CEU][hapmap];0.89[EUR][1000 genomes]
rs10964943	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10964952	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10964957	1.00[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10964959	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10964961	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1112783	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12551190	0.93[CEU][hapmap];0.89[EUR][1000 genomes]
rs12552812	0.85[EUR][1000 genomes]
rs12553763	0.93[CEU][hapmap];0.89[EUR][1000 genomes]
rs12553910	0.94[EUR][1000 genomes]
rs12555631	0.93[CEU][hapmap]
rs12555749	0.84[EUR][1000 genomes]
rs1330312	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1330313	0.81[CEU][hapmap]
rs1330314	1.00[CEU][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs1330317	0.82[EUR][1000 genomes]
rs1411436	0.93[CEU][hapmap];0.89[EUR][1000 genomes]
rs1424854	1.00[CEU][hapmap]
rs1590897	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1590898	0.83[EUR][1000 genomes]
rs1820313	0.93[CEU][hapmap]
rs1831391	0.93[CEU][hapmap]
rs1834247	0.93[CEU][hapmap]
rs1854700	0.93[CEU][hapmap]
rs1928854	0.93[CEU][hapmap];0.89[EUR][1000 genomes]
rs1928855	0.88[EUR][1000 genomes]
rs1928856	0.87[EUR][1000 genomes]
rs1952690	0.96[EUR][1000 genomes]
rs2007448	0.82[EUR][1000 genomes]
rs2015345	0.93[CEU][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap]
rs2098814	0.93[CEU][hapmap]
rs2225329	0.83[EUR][1000 genomes]
rs28437205	0.88[EUR][1000 genomes]
rs2939	0.93[CEU][hapmap];0.91[GIH][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap]
rs2988573	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2988574	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2990140	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[EUR][1000 genomes]
rs2990141	0.84[CEU][hapmap]
rs3750479	0.93[CEU][hapmap]
rs3758236	1.00[CEU][hapmap]
rs3955236	0.93[CEU][hapmap]
rs4007646	0.81[EUR][1000 genomes]
rs4112794	0.89[EUR][1000 genomes]
rs4568686	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4582643	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4628333	0.93[CEU][hapmap];0.89[EUR][1000 genomes]
rs4977682	0.93[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap]
rs4977684	0.93[CEU][hapmap]
rs4977714	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4978069	0.82[EUR][1000 genomes]
rs56035072	0.83[EUR][1000 genomes]
rs57122438	0.89[EUR][1000 genomes]
rs57146220	0.89[EUR][1000 genomes]
rs57371737	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs583396	0.95[EUR][1000 genomes]
rs596180	0.93[CEU][hapmap];0.81[GIH][hapmap]
rs597440	0.91[EUR][1000 genomes]
rs604762	0.93[CEU][hapmap];0.94[CHB][hapmap];0.81[GIH][hapmap];0.90[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs612966	1.00[CEU][hapmap];0.94[CHB][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs614541	1.00[CEU][hapmap];0.94[CHB][hapmap];0.81[GIH][hapmap];0.90[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs618507	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs637700	0.95[EUR][1000 genomes]
rs637949	0.93[CEU][hapmap];0.81[GIH][hapmap];0.82[TSI][hapmap]
rs6475510	0.81[EUR][1000 genomes]
rs6475527	0.81[ASN][1000 genomes]
rs653778	0.87[EUR][1000 genomes]
rs660675	0.91[EUR][1000 genomes]
rs667214	0.94[EUR][1000 genomes]
rs667635	0.94[EUR][1000 genomes]
rs681680	0.95[EUR][1000 genomes]
rs7019617	0.92[CEU][hapmap]
rs7019739	0.93[CEU][hapmap]
rs7030705	0.93[CEU][hapmap]
rs7031048	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs7032044	0.86[ASN][1000 genomes]
rs7033839	0.93[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap]
rs7035639	0.93[CEU][hapmap]
rs7037147	0.93[CEU][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap]
rs7041635	0.93[CEU][hapmap]
rs7043560	0.82[EUR][1000 genomes]
rs7046898	0.82[EUR][1000 genomes]
rs7047240	0.82[EUR][1000 genomes]
rs7047805	0.86[CEU][hapmap]
rs7047811	0.93[CEU][hapmap];0.91[GIH][hapmap];0.89[TSI][hapmap]
rs73418252	0.88[EUR][1000 genomes]
rs768848	0.82[EUR][1000 genomes]
rs768849	0.93[CEU][hapmap];0.82[EUR][1000 genomes]
rs7848803	0.87[EUR][1000 genomes]
rs7849623	0.93[CEU][hapmap];0.95[TSI][hapmap]
rs7849862	0.93[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap]
rs7849902	0.86[ASN][1000 genomes]
rs7852809	0.82[EUR][1000 genomes]
rs7854247	0.93[CEU][hapmap]
rs7857863	0.85[EUR][1000 genomes]
rs7866359	0.93[CEU][hapmap];0.80[EUR][1000 genomes]
rs7866640	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[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	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	nsv892734	chr9:21108817-21323089	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10117202	KLHL9	cis	multi-tissue	Pritchard
rs10117202	KLHL9	cis	lymphoblastoid	seeQTL

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21316600-21330600	Weak transcription	Small Intestine	intestine
2	chr9:21317000-21326800	Weak transcription	Hela-S3	cervix
3	chr9:21317200-21331600	Weak transcription	Esophagus	oesophagus
4	chr9:21317200-21331600	Weak transcription	Gastric	stomach
5	chr9:21318200-21330000	Weak transcription	Brain Anterior Caudate	brain
6	chr9:21318200-21330400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr9:21318800-21324000	Weak transcription	NHEK	skin
8	chr9:21318800-21326800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr9:21318800-21326800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr9:21318800-21330600	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr9:21318800-21331000	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr9:21318800-21331200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr9:21318800-21331800	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr9:21318800-21332600	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr9:21318800-21332800	Weak transcription	Fetal Kidney	kidney
16	chr9:21319000-21326000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr9:21319000-21326800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr9:21319000-21332200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr9:21319000-21333200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr9:21319400-21329400	Weak transcription	Fetal Heart	heart
21	chr9:21319600-21323200	Weak transcription	HSMMtube	muscle
22	chr9:21319600-21333200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr9:21319800-21326000	Weak transcription	Fetal Brain Male	brain
24	chr9:21320000-21324600	Strong transcription	Primary T cells from cord blood	blood
25	chr9:21320000-21325600	Weak transcription	Rectal Smooth Muscle	rectum
26	chr9:21320200-21323200	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr9:21320200-21326400	Strong transcription	HSMM	muscle
28	chr9:21320600-21323800	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr9:21320600-21324400	Strong transcription	Liver	Liver
30	chr9:21320600-21326000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr9:21320600-21326200	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr9:21320600-21331600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr9:21320800-21326200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr9:21321000-21326800	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr9:21321200-21324000	Strong transcription	Placenta	Placenta
36	chr9:21321200-21324200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr9:21321200-21324200	Strong transcription	Colon Smooth Muscle	Colon
38	chr9:21321200-21324200	Strong transcription	Fetal Thymus	thymus
39	chr9:21321200-21324400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr9:21321200-21324400	Strong transcription	Primary B cells from cord blood	blood
41	chr9:21321200-21324400	Strong transcription	Primary T helper cells PMA-I stimulated	--
42	chr9:21321200-21324400	Strong transcription	Brain Hippocampus Middle	brain
43	chr9:21321200-21324800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr9:21321200-21324800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr9:21321200-21324800	Strong transcription	Adipose Nuclei	Adipose
46	chr9:21321200-21324800	Strong transcription	Fetal Muscle Trunk	muscle
47	chr9:21321200-21324800	Strong transcription	Fetal Muscle Leg	muscle
48	chr9:21321200-21325000	Strong transcription	Fetal Brain Female	brain
49	chr9:21321200-21325000	Strong transcription	Fetal Intestine Small	intestine
50	chr9:21321200-21325200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links