Variant report

Variant	rs12683349
Chromosome Location	chr9:21316313-21316314
allele	C/T
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	CEBPB	chr9:21316276-21316754	Hela-S3	cervix:	n/a	n/a
2	ZNF263	chr9:21316253-21317026	HEK293-T-REx	kidney:	n/a	n/a

Variant related genes	Relation type
IFNA20P	TF binding region

Extended variants
information (count: 74 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10113879	0.97[ASN][1000 genomes]
rs10116615	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10117677	1.00[CEU][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10119678	0.82[CEU][hapmap];0.82[CHB][hapmap];0.92[YRI][hapmap]
rs10120675	0.97[ASN][1000 genomes]
rs10125010	0.94[CEU][hapmap]
rs10738591	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10757208	0.96[ASN][1000 genomes]
rs10757210	0.97[ASN][1000 genomes]
rs10757212	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10757213	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10811505	0.94[CEU][hapmap]
rs10811519	0.96[ASN][1000 genomes]
rs10811522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10811523	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10811529	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10964953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10964954	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10964955	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10964956	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10964958	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10964960	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10964966	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12237982	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1224392	0.90[EUR][1000 genomes]
rs12553910	0.80[ASN][1000 genomes]
rs1330311	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1330313	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1330314	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1330323	0.96[ASN][1000 genomes]
rs1330324	0.96[ASN][1000 genomes]
rs1360286	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1411437	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1467734	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]
rs1467735	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1467736	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1475547	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1475548	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1543874	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[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];0.98[ASN][1000 genomes]
rs2094787	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2094788	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2480927	0.90[EUR][1000 genomes]
rs3758236	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4406500	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[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];0.99[ASN][1000 genomes]
rs4978093	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4978097	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[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];0.97[ASN][1000 genomes]
rs7020867	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7021699	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7031048	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs7032044	0.94[EUR][1000 genomes]
rs7035600	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7035669	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7849902	0.93[EUR][1000 genomes]
rs7853081	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7858766	0.96[ASN][1000 genomes]
rs7862940	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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	0.96[ASN][1000 genomes]
rs8729	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]
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	nsv613757	chr9:21289923-21316649	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh	TF binding region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12683349	KLHL9	cis	multi-tissue	Pritchard
rs12683349	KLHL9	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21309800-21322600	Weak transcription	Brain Substantia Nigra	brain
2	chr9:21312200-21316400	Weak transcription	Esophagus	oesophagus
3	chr9:21312200-21322000	Weak transcription	GM12878-XiMat	blood
4	chr9:21313400-21317800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr9:21313600-21316400	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr9:21315000-21323000	Weak transcription	Thymus	Thymus
7	chr9:21316000-21317000	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr9:21316200-21316400	Enhancers	Stomach Smooth Muscle	stomach
9	chr9:21316200-21316400	Bivalent Enhancer	Osteobl	bone
10	chr9:21316200-21316600	Flanking Active TSS	Liver	Liver
11	chr9:21316200-21316800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr9:21316200-21316800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr9:21316200-21316800	Flanking Active TSS	Hela-S3	cervix
14	chr9:21316200-21317000	Enhancers	Adipose Nuclei	Adipose
15	chr9:21316200-21317400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr9:21316200-21317400	Enhancers	HMEC	breast
17	chr9:21316200-21318600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr9:21316200-21322800	Weak transcription	Fetal Lung	lung

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