Variant report

Variant	rs10967560
Chromosome Location	chr9:26845303-26845304
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:26844492..26846468-chr9:26891294..26892870,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000120159	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1011358	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10511796	0.95[CHB][hapmap]
rs10812478	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10812480	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10812485	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10812509	0.84[CHB][hapmap]
rs10812510	0.85[CHB][hapmap]
rs10812517	0.84[CHB][hapmap]
rs10967541	1.00[CEU][hapmap];0.84[CHB][hapmap];0.90[EUR][1000 genomes]
rs10967550	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10967565	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10967566	0.82[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10967575	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10967581	1.00[CHB][hapmap];0.89[JPT][hapmap];0.95[ASN][1000 genomes]
rs10967586	0.95[CHB][hapmap]
rs10967621	0.85[CHB][hapmap]
rs10967627	0.85[CHB][hapmap]
rs10967630	0.85[CHB][hapmap]
rs10967633	0.85[CHB][hapmap]
rs10967635	0.84[CHB][hapmap]
rs10967650	0.85[CHB][hapmap]
rs10967678	0.85[CHB][hapmap]
rs12238317	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12345197	0.81[ASN][1000 genomes]
rs1336337	0.94[CHB][hapmap]
rs17760657	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17760820	0.95[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs2184739	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3737226	0.90[CHB][hapmap]
rs3739544	0.85[CHB][hapmap]
rs3739547	0.94[CHB][hapmap]
rs3739550	0.95[CHB][hapmap]
rs4316229	0.91[ASN][1000 genomes]
rs7018943	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7019034	0.90[CHB][hapmap]
rs7035447	0.84[CHB][hapmap]
rs7857447	0.84[CHB][hapmap]
rs7857466	0.90[CHB][hapmap]
rs7869798	0.95[CHB][hapmap]
rs7871868	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7873073	0.90[CHB][hapmap]
rs7874940	0.85[CHB][hapmap]
rs7875171	0.85[CHB][hapmap]
rs9644870	0.84[CHB][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
rs10967560	IFT74	cis	Thyroid	GTEx

Chromatin state (count:111 , 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	chr9:26822600-26846200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr9:26830200-26865400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr9:26832200-26866800	Weak transcription	Gastric	stomach
5	chr9:26832200-26878400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr9:26834000-26882400	Weak transcription	HUVEC	blood vessel
7	chr9:26834200-26849800	Weak transcription	Fetal Thymus	thymus
8	chr9:26834200-26852800	Weak transcription	Fetal Muscle Trunk	muscle
9	chr9:26834200-26852800	Weak transcription	HSMMtube	muscle
10	chr9:26834200-26853400	Weak transcription	Fetal Muscle Leg	muscle
11	chr9:26834200-26854800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr9:26834200-26855000	Weak transcription	Ovary	ovary
13	chr9:26834200-26858800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr9:26834200-26859000	Weak transcription	Fetal Kidney	kidney
15	chr9:26834200-26870600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr9:26834200-26878400	Weak transcription	Brain Angular Gyrus	brain
17	chr9:26834200-26878600	Weak transcription	Spleen	Spleen
18	chr9:26834200-26880200	Weak transcription	Lung	lung
19	chr9:26834200-26880200	Weak transcription	NHEK	skin
20	chr9:26834200-26882200	Weak transcription	HMEC	breast
21	chr9:26834200-26888200	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr9:26834200-26891200	Weak transcription	NHDF-Ad	bronchial
23	chr9:26834400-26854800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr9:26836200-26854200	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr9:26836400-26849000	Weak transcription	Primary B cells from cord blood	blood
26	chr9:26836400-26855000	Weak transcription	Brain Hippocampus Middle	brain
27	chr9:26836400-26859000	Weak transcription	Fetal Brain Male	brain
28	chr9:26836400-26879600	Weak transcription	Esophagus	oesophagus
29	chr9:26836600-26891400	Weak transcription	Brain Substantia Nigra	brain
30	chr9:26837400-26848800	Weak transcription	Hela-S3	cervix
31	chr9:26837400-26855200	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr9:26837800-26855800	Weak transcription	Osteobl	bone
33	chr9:26838000-26878200	Weak transcription	Brain Germinal Matrix	brain
34	chr9:26838200-26853000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr9:26838200-26858800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr9:26838200-26879600	Weak transcription	Pancreas	Pancrea
37	chr9:26838400-26852800	Weak transcription	Aorta	Aorta
38	chr9:26838600-26854600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr9:26838800-26852800	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr9:26838800-26852800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr9:26839000-26858600	Weak transcription	Small Intestine	intestine
42	chr9:26839400-26855600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr9:26839600-26854600	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr9:26839600-26855000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr9:26839800-26846800	Weak transcription	Fetal Intestine Small	intestine
46	chr9:26840000-26846200	Strong transcription	Liver	Liver
47	chr9:26840600-26847800	Weak transcription	GM12878-XiMat	blood
48	chr9:26840600-26859000	Weak transcription	Fetal Brain Female	brain
49	chr9:26840600-26882400	Weak transcription	Brain Cingulate Gyrus	brain
50	chr9:26840800-26855200	Weak transcription	Fetal Lung	lung

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