Variant report

Variant	rs7872479
Chromosome Location	chr9:21330522-21330523
allele	G/T
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: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10116615	0.94[EUR][1000 genomes]
rs10117677	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10757212	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10757213	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10811522	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10811523	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10964953	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	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	0.81[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	0.93[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	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1360286	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1411437	0.85[EUR][1000 genomes]
rs1467734	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1467735	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1467736	0.89[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	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1831390	0.85[EUR][1000 genomes]
rs2094787	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2094788	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2480927	0.91[EUR][1000 genomes]
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	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]
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]
rs7849902	0.92[EUR][1000 genomes]
rs7853081	0.99[EUR][1000 genomes]
rs7862940	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8729	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];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	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7872479	KLHL9	Cis_1M	lymphoblastoid	RTeQTL
rs7872479	KLHL9	cis	multi-tissue	Pritchard

Chromatin state (count:117 , 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	chr9:21317200-21331600	Weak transcription	Esophagus	oesophagus
3	chr9:21317200-21331600	Weak transcription	Gastric	stomach
4	chr9:21318800-21330600	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr9:21318800-21331000	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr9:21318800-21331200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr9:21318800-21331800	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr9:21318800-21332600	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr9:21318800-21332800	Weak transcription	Fetal Kidney	kidney
10	chr9:21319000-21332200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr9:21319000-21333200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr9:21319600-21333200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr9:21320600-21331600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr9:21321400-21331600	Weak transcription	Spleen	Spleen
15	chr9:21321600-21333400	Weak transcription	Colonic Mucosa	Colon
16	chr9:21322000-21331600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr9:21322000-21331600	Weak transcription	HepG2	liver
18	chr9:21322200-21333600	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr9:21323400-21331800	Weak transcription	Aorta	Aorta
20	chr9:21323400-21333800	Weak transcription	Lung	lung
21	chr9:21323600-21330800	Weak transcription	Pancreas	Pancrea
22	chr9:21323600-21331600	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr9:21323800-21331800	Weak transcription	Stomach Smooth Muscle	stomach
24	chr9:21324000-21331400	Weak transcription	Right Ventricle	heart
25	chr9:21324000-21333000	Weak transcription	Placenta	Placenta
26	chr9:21324200-21331600	Weak transcription	Fetal Thymus	thymus
27	chr9:21324200-21331600	Weak transcription	A549	lung
28	chr9:21324400-21330800	Weak transcription	Ovary	ovary
29	chr9:21324400-21331600	Weak transcription	Thymus	Thymus
30	chr9:21324400-21333200	Weak transcription	Primary B cells from cord blood	blood
31	chr9:21324400-21333200	Weak transcription	Fetal Stomach	stomach
32	chr9:21324400-21333400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr9:21324800-21331000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr9:21324800-21331400	Weak transcription	NHLF	lung
35	chr9:21324800-21331600	Weak transcription	Primary B cells from peripheral blood	blood
36	chr9:21324800-21331600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr9:21324800-21333000	Weak transcription	Fetal Intestine Large	intestine
38	chr9:21324800-21333000	Weak transcription	Fetal Muscle Trunk	muscle
39	chr9:21324800-21333000	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr9:21324800-21333200	Weak transcription	Primary hematopoietic stem cells	blood
41	chr9:21325000-21331600	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr9:21325000-21333000	Weak transcription	Fetal Intestine Small	intestine
43	chr9:21325200-21331600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr9:21325200-21331600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr9:21326000-21331000	Weak transcription	Duodenum Mucosa	Duodenum
46	chr9:21326200-21330600	Weak transcription	NHEK	skin
47	chr9:21326200-21333000	Weak transcription	HSMMtube	muscle
48	chr9:21326800-21333000	Enhancers	Primary T helper naive cells from peripheral blood	blood
49	chr9:21326800-21333200	Enhancers	Colon Smooth Muscle	Colon
50	chr9:21326800-21333400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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