Variant report

Variant	rs1467734
Chromosome Location	chr9:21318832-21318833
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr9:21318161-21319042	H1-neurons	neurons:	n/a	n/a
2	CTCF	chr9:21318226-21318893	HCT-116	colon:	n/a	chr9:21318469-21318485 chr9:21318468-21318486 chr9:21318470-21318491 chr9:21318471-21318484
3	CTCF	chr9:21318820-21318970	A549	lung:	n/a	n/a
4	SMC3	chr9:21318256-21318875	GM12878	blood:	n/a	chr9:21318470-21318484 chr9:21318607-21318615
5	RAD21	chr9:21318200-21318840	HCT-116	colon:	n/a	chr9:21318469-21318488
6	POLR2A	chr9:21318651-21319038	H1-neurons	neurons:	n/a	n/a
7	CTCF	chr9:21318760-21318910	GM12871	blood:	n/a	n/a
8	SMC3	chr9:21318168-21319039	SK-N-SH	brain:	n/a	chr9:21318470-21318484 chr9:21318607-21318615
9	CTCF	chr9:21318740-21318890	RPTEC	kidney:	n/a	n/a
10	REST	chr9:21318359-21319027	H1-neurons	neurons:	n/a	n/a
11	RFX5	chr9:21318228-21319070	SK-N-SH	brain:	n/a	n/a
12	CTCF	chr9:21318135-21319004	A549	lung:	n/a	chr9:21318469-21318485 chr9:21318468-21318486 chr9:21318470-21318491 chr9:21318471-21318484
13	CTCF	chr9:21318760-21318910	HepG2	liver:	n/a	n/a
14	CTCF	chr9:21318800-21318950	HVMF	connective:	n/a	n/a
15	CTCF	chr9:21318820-21318970	GM12864	blood:	n/a	n/a
16	RAD21	chr9:21317967-21318892	SK-N-SH	brain:	n/a	chr9:21318469-21318488
17	MYC	chr9:21318239-21318973	NB4	blood:	n/a	n/a
18	CTCF	chr9:21318820-21318970	AG04450	lung:	n/a	n/a
19	CTCF	chr9:21318800-21318950	HBMEC	blood vessel:	n/a	n/a
20	CTCF	chr9:21317947-21318977	SK-N-SH	brain:	n/a	chr9:21318469-21318485 chr9:21318468-21318486 chr9:21318470-21318491 chr9:21318471-21318484

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:21318010..21319069-chr9:21395893..21396720,4	MCF-7	breast:
2	chr9:21253305..21254010-chr9:21318409..21318973,2	MCF-7	breast:

Variant related genes	Relation type
IFNA20P	TF binding region
ENSG00000261696	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10113879	0.82[ASN][1000 genomes]
rs10116615	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10117677	1.00[CEU][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10119678	0.82[CEU][hapmap];0.92[YRI][hapmap]
rs10120675	0.82[ASN][1000 genomes]
rs10125010	0.94[CEU][hapmap]
rs10738591	0.95[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs10757208	0.82[ASN][1000 genomes]
rs10757210	0.82[ASN][1000 genomes]
rs10757212	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10757213	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10811505	0.94[CEU][hapmap]
rs10811519	0.82[ASN][1000 genomes]
rs10811522	1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10811523	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10811529	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10964953	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10964954	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10964955	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10964956	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10964958	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10964960	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10964966	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12237982	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1224392	0.90[EUR][1000 genomes]
rs12683349	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1330311	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1330313	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1330314	0.95[CHB][hapmap];0.85[JPT][hapmap];0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1330323	0.82[ASN][1000 genomes]
rs1330324	0.82[ASN][1000 genomes]
rs1360286	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1411437	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1467735	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1467736	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1475547	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1475548	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1543874	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1820314	0.90[CEU][hapmap]
rs1831390	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1952690	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2094787	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2094788	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2480927	0.90[EUR][1000 genomes]
rs3758236	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs4406500	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4978056	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4978092	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4978093	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4978097	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs600118	0.97[EUR][1000 genomes]
rs616873	0.94[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6475527	0.92[EUR][1000 genomes]
rs667069	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs67212517	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7020867	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7021699	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7031048	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs7032044	0.94[EUR][1000 genomes]
rs7035600	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7035669	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7849902	0.93[EUR][1000 genomes]
rs7853081	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7858766	0.82[ASN][1000 genomes]
rs7862940	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7868334	0.94[CEU][hapmap]
rs7872479	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7872575	0.82[ASN][1000 genomes]
rs8729	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]
rs9298814	0.94[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	esv3429264	chr9:21318302-21321050	Weak transcription Enhancers Strong transcription Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1467734	KLHL9	cis	multi-tissue	Pritchard
rs1467734	KLHL9	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21309800-21322600	Weak transcription	Brain Substantia Nigra	brain
2	chr9:21312200-21322000	Weak transcription	GM12878-XiMat	blood
3	chr9:21315000-21323000	Weak transcription	Thymus	Thymus
4	chr9:21316200-21322800	Weak transcription	Fetal Lung	lung
5	chr9:21316400-21319000	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr9:21316400-21322800	Weak transcription	Stomach Smooth Muscle	stomach
7	chr9:21316600-21321200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr9:21316600-21322600	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr9:21316600-21322600	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr9:21316600-21322800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr9:21316600-21322800	Weak transcription	Lung	lung
12	chr9:21316600-21323000	Weak transcription	Pancreas	Pancrea
13	chr9:21316600-21330600	Weak transcription	Small Intestine	intestine
14	chr9:21316800-21319000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr9:21316800-21322800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr9:21317000-21320400	Weak transcription	Brain Hippocampus Middle	brain
17	chr9:21317000-21321200	Weak transcription	Primary B cells from cord blood	blood
18	chr9:21317000-21321200	Weak transcription	Colon Smooth Muscle	Colon
19	chr9:21317000-21326800	Weak transcription	Hela-S3	cervix
20	chr9:21317200-21320600	Weak transcription	Liver	Liver
21	chr9:21317200-21322800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr9:21317200-21323000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr9:21317200-21323000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr9:21317200-21331600	Weak transcription	Esophagus	oesophagus
25	chr9:21317200-21331600	Weak transcription	Gastric	stomach
26	chr9:21317400-21321400	Weak transcription	Osteobl	bone
27	chr9:21317400-21323000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr9:21317600-21321600	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr9:21317800-21319000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr9:21317800-21319000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr9:21318000-21319000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr9:21318200-21321200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr9:21318200-21330000	Weak transcription	Brain Anterior Caudate	brain
34	chr9:21318200-21330400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr9:21318400-21319000	Enhancers	Primary T helper naive cells from peripheral blood	blood
36	chr9:21318400-21320000	Weak transcription	Primary T cells from cord blood	blood
37	chr9:21318600-21319000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr9:21318600-21319000	Enhancers	H9 Cell Line	embryonic stem cell
39	chr9:21318600-21319000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr9:21318600-21319000	Enhancers	A549	lung
41	chr9:21318600-21319000	Enhancers	HUVEC	blood vessel
42	chr9:21318600-21321200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr9:21318600-21321200	Weak transcription	Aorta	Aorta
44	chr9:21318800-21319000	Enhancers	iPS-20b Cell Line	embryonic stem cell
45	chr9:21318800-21319000	Enhancers	Fetal Muscle Leg	muscle
46	chr9:21318800-21320200	Weak transcription	HSMM	muscle
47	chr9:21318800-21320400	Weak transcription	Brain Cingulate Gyrus	brain
48	chr9:21318800-21320600	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr9:21318800-21320800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr9:21318800-21321200	Weak transcription	Primary T helper cells PMA-I stimulated	--

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