Variant report

Variant	rs17760657
Chromosome Location	chr9:26832939-26832940
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1011358	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10511796	0.89[CHB][hapmap]
rs10757630	0.83[CHB][hapmap]
rs10812478	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10812480	1.00[CEU][hapmap];0.84[CHB][hapmap];0.90[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10812485	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10812494	0.85[JPT][hapmap];0.89[YRI][hapmap]
rs10812509	0.84[JPT][hapmap]
rs10812510	0.80[JPT][hapmap]
rs10967541	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[GIH][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes]
rs10967550	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10967560	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10967565	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10967566	0.82[CEU][hapmap];0.89[CHB][hapmap];0.90[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10967575	1.00[CEU][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10967581	0.84[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.89[YRI][hapmap];0.90[ASN][1000 genomes]
rs10967586	0.90[CHB][hapmap]
rs10967597	0.80[JPT][hapmap];0.89[YRI][hapmap]
rs10967611	0.84[ASW][hapmap];0.91[MEX][hapmap];0.89[YRI][hapmap]
rs10967627	0.80[JPT][hapmap]
rs10967630	0.80[JPT][hapmap]
rs10967633	0.80[JPT][hapmap]
rs10967635	0.82[CHD][hapmap];0.80[JPT][hapmap];0.92[MEX][hapmap]
rs10967649	0.84[CHD][hapmap];0.91[MEX][hapmap]
rs12236850	0.82[CHD][hapmap];0.92[MEX][hapmap]
rs12238317	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1336337	0.88[CHB][hapmap];0.84[JPT][hapmap]
rs17760820	0.89[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.83[ASN][1000 genomes]
rs17833941	0.84[JPT][hapmap];0.89[YRI][hapmap]
rs2184739	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3737226	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs3739544	0.80[JPT][hapmap]
rs3739547	0.84[ASW][hapmap];0.89[CHB][hapmap];0.84[CHD][hapmap];0.85[JPT][hapmap];0.92[MEX][hapmap];0.89[YRI][hapmap]
rs3739550	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs4316229	0.86[ASN][1000 genomes]
rs7018943	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7019034	0.85[CHB][hapmap];0.85[JPT][hapmap];0.89[YRI][hapmap]
rs7019075	0.85[YRI][hapmap]
rs7035447	0.82[CHD][hapmap];0.80[JPT][hapmap];0.92[MEX][hapmap]
rs7857447	0.80[JPT][hapmap]
rs7857466	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs7857990	0.89[YRI][hapmap]
rs7869798	0.89[CHB][hapmap]
rs7871868	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7873073	0.84[ASW][hapmap];0.85[CHB][hapmap];0.84[CHD][hapmap];0.85[JPT][hapmap];0.92[MEX][hapmap];0.89[YRI][hapmap]
rs7874940	0.80[JPT][hapmap]
rs7875171	0.80[JPT][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	nsv1026827	chr9:26693515-26904699	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	esv3373096	chr9:26825001-26848031	Weak transcription ZNF genes & repeats Strong transcription Enhancers	Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17760657	IFT74	cis	Thyroid	GTEx

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:26822200-26889400	Weak transcription	Psoas Muscle	Psoas
2	chr9:26822600-26846200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr9:26829000-26833400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr9:26829000-26839400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr9:26829000-26839600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr9:26829000-26840200	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr9:26829000-26840400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr9:26829200-26842200	Weak transcription	Left Ventricle	heart
9	chr9:26830200-26865400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr9:26830400-26833800	Weak transcription	HSMMtube	muscle
11	chr9:26832200-26866800	Weak transcription	Gastric	stomach
12	chr9:26832200-26878400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr9:26832800-26833000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
14	chr9:26832800-26834200	Enhancers	Fetal Kidney	kidney

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