Variant report

Variant	rs6475945
Chromosome Location	chr9:26866230-26866231
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:26865662..26868224-chr9:26870486..26872108,2	MCF-7	breast:

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10738762	0.89[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10757635	0.89[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10757636	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10812479	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10812482	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10812487	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10812488	0.89[CEU][hapmap];0.88[JPT][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10812494	0.81[JPT][hapmap]
rs10812500	0.83[CEU][hapmap]
rs10812503	0.85[CEU][hapmap];0.94[JPT][hapmap]
rs10812507	0.86[CEU][hapmap];0.95[JPT][hapmap]
rs10812509	0.80[JPT][hapmap]
rs10812518	0.94[JPT][hapmap]
rs10967548	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10967549	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10967551	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10967556	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10967586	0.90[JPT][hapmap]
rs10967594	0.83[CEU][hapmap]
rs10967652	0.86[CEU][hapmap];0.95[JPT][hapmap]
rs10967679	0.95[JPT][hapmap]
rs12004732	0.83[CEU][hapmap]
rs12342005	0.89[CEU][hapmap]
rs12345197	0.83[AMR][1000 genomes]
rs1541144	0.86[CEU][hapmap];0.95[JPT][hapmap]
rs16910895	0.84[CEU][hapmap]
rs17833941	0.81[JPT][hapmap]
rs3737226	0.81[JPT][hapmap]
rs3739547	0.80[JPT][hapmap]
rs3739550	0.81[JPT][hapmap]
rs3758218	0.85[CEU][hapmap];0.94[JPT][hapmap]
rs4316229	0.83[AMR][1000 genomes]
rs4413873	0.86[CEU][hapmap];0.82[JPT][hapmap]
rs4621911	0.95[JPT][hapmap]
rs59159685	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62544398	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6475944	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6475946	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6475947	1.00[CEU][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6475948	0.83[CEU][hapmap]
rs6475954	0.95[JPT][hapmap]
rs7018585	0.86[CEU][hapmap];0.95[JPT][hapmap]
rs7019034	0.81[JPT][hapmap]
rs7020010	0.85[JPT][hapmap]
rs7032756	0.94[CEU][hapmap];0.87[CHB][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7033238	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7034670	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7035292	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7038218	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7040516	0.84[CEU][hapmap]
rs7042133	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7042447	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7849248	0.84[JPT][hapmap]
rs7856462	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7857466	0.81[JPT][hapmap]
rs7857481	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7857669	0.94[JPT][hapmap]
rs7860542	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs7863476	0.94[CEU][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7868158	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7870787	0.85[JPT][hapmap]
rs7871668	0.95[JPT][hapmap]
rs7872496	0.90[JPT][hapmap]
rs7873073	0.80[JPT][hapmap]
rs7875068	0.86[CEU][hapmap];0.95[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6475945	IFT74	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:26822200-26889400	Weak transcription	Psoas Muscle	Psoas
2	chr9:26832200-26866800	Weak transcription	Gastric	stomach
3	chr9:26832200-26878400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr9:26834000-26882400	Weak transcription	HUVEC	blood vessel
5	chr9:26834200-26870600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr9:26834200-26878400	Weak transcription	Brain Angular Gyrus	brain
7	chr9:26834200-26878600	Weak transcription	Spleen	Spleen
8	chr9:26834200-26880200	Weak transcription	Lung	lung
9	chr9:26834200-26880200	Weak transcription	NHEK	skin
10	chr9:26834200-26882200	Weak transcription	HMEC	breast
11	chr9:26834200-26888200	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr9:26834200-26891200	Weak transcription	NHDF-Ad	bronchial
13	chr9:26836400-26879600	Weak transcription	Esophagus	oesophagus
14	chr9:26836600-26891400	Weak transcription	Brain Substantia Nigra	brain
15	chr9:26838000-26878200	Weak transcription	Brain Germinal Matrix	brain
16	chr9:26838200-26879600	Weak transcription	Pancreas	Pancrea
17	chr9:26840600-26882400	Weak transcription	Brain Cingulate Gyrus	brain
18	chr9:26840800-26879800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr9:26841200-26879800	Weak transcription	Colonic Mucosa	Colon
20	chr9:26842600-26882200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr9:26842800-26879600	Weak transcription	Thymus	Thymus
22	chr9:26843200-26878400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr9:26846400-26870600	Weak transcription	Fetal Stomach	stomach
24	chr9:26846600-26881600	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr9:26847000-26883000	Weak transcription	K562	blood
26	chr9:26851400-26878600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr9:26851400-26888000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr9:26851800-26888600	Weak transcription	Fetal Heart	heart
29	chr9:26851800-26891600	Weak transcription	Stomach Mucosa	stomach
30	chr9:26852400-26888000	Weak transcription	NHLF	lung
31	chr9:26852800-26876000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr9:26853200-26878600	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr9:26853600-26878200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr9:26853800-26870600	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr9:26853800-26878400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr9:26853800-26878400	Weak transcription	Aorta	Aorta
37	chr9:26855000-26882200	Weak transcription	Right Ventricle	heart
38	chr9:26855400-26880200	Weak transcription	HepG2	liver
39	chr9:26855800-26888200	Weak transcription	NH-A	brain
40	chr9:26856000-26878800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr9:26856000-26881600	Weak transcription	Brain Hippocampus Middle	brain
42	chr9:26856000-26882200	Weak transcription	Brain Anterior Caudate	brain
43	chr9:26856000-26882200	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr9:26856200-26878400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr9:26856200-26881400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr9:26856400-26878600	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr9:26856600-26878600	Weak transcription	Rectal Smooth Muscle	rectum
48	chr9:26856600-26888400	Weak transcription	Osteobl	bone
49	chr9:26857200-26868200	Weak transcription	GM12878-XiMat	blood
50	chr9:26857600-26866600	Weak transcription	Left Ventricle	heart

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