Variant report

Variant	rs10967652
Chromosome Location	chr9:27000340-27000341
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10738762	0.95[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10757635	0.95[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10757636	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10812488	1.00[CEU][hapmap];0.83[CHB][hapmap];0.83[JPT][hapmap];0.84[YRI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10812503	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10812504	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10812507	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10812508	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10812509	0.80[JPT][hapmap];0.83[ASN][1000 genomes]
rs10812510	0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs10812515	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10812516	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10812517	0.81[JPT][hapmap]
rs10812518	0.83[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10812519	0.86[ASN][1000 genomes]
rs10812523	0.86[ASN][1000 genomes]
rs10967586	0.85[JPT][hapmap]
rs10967621	0.81[JPT][hapmap]
rs10967627	0.81[JPT][hapmap]
rs10967629	0.84[ASN][1000 genomes]
rs10967630	0.81[JPT][hapmap]
rs10967632	0.84[ASN][1000 genomes]
rs10967633	0.81[JPT][hapmap]
rs10967635	0.80[JPT][hapmap]
rs10967645	0.89[CHB][hapmap];0.85[ASN][1000 genomes]
rs10967646	0.82[ASN][1000 genomes]
rs10967648	0.96[ASN][1000 genomes]
rs10967649	0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs10967650	0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs10967670	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10967678	0.81[JPT][hapmap]
rs10967679	0.84[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10967680	0.88[ASN][1000 genomes]
rs12337896	0.83[CHB][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1541144	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17833941	0.81[JPT][hapmap]
rs1819539	0.84[CHB][hapmap];0.85[JPT][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2184438	0.86[ASN][1000 genomes]
rs2184439	0.84[ASN][1000 genomes]
rs2225720	0.84[CHB][hapmap];0.85[JPT][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3739544	0.81[JPT][hapmap]
rs3758218	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4413873	1.00[CEU][hapmap];0.89[CHB][hapmap];0.88[JPT][hapmap];0.97[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4463511	0.85[ASN][1000 genomes]
rs4621911	0.84[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs56307252	0.80[ASN][1000 genomes]
rs59159685	0.80[ASN][1000 genomes]
rs6475945	0.86[CEU][hapmap];0.95[JPT][hapmap]
rs6475947	0.86[CEU][hapmap];0.84[YRI][hapmap]
rs6475954	0.84[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7018585	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7020010	0.94[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs7034115	0.85[ASN][1000 genomes]
rs7034478	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7034670	0.81[AMR][1000 genomes]
rs7035447	0.80[JPT][hapmap]
rs7038218	0.89[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7040505	0.85[JPT][hapmap];0.97[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7042133	0.81[ASN][1000 genomes]
rs7042447	0.86[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs7045747	0.87[ASN][1000 genomes]
rs7849248	0.94[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs7854191	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7856462	0.86[CEU][hapmap];0.95[JPT][hapmap]
rs7857447	0.81[JPT][hapmap]
rs7857669	0.83[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7860542	0.82[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs7863476	0.90[CEU][hapmap];0.94[JPT][hapmap];0.83[YRI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7868158	0.85[CEU][hapmap];0.94[JPT][hapmap]
rs7870787	0.89[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs7871668	0.84[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7872496	0.85[JPT][hapmap]
rs7874940	0.81[JPT][hapmap]
rs7875068	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7875171	0.81[JPT][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	nsv528614	chr9:26893662-27074233	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv517269	chr9:26945976-27137242	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv892862	chr9:26956663-27190655	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10967652	IFT74	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:26957000-27024000	Weak transcription	Esophagus	oesophagus
2	chr9:26957200-27026600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr9:26957200-27040000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr9:26974200-27023600	Weak transcription	Fetal Brain Female	brain
5	chr9:26976200-27003600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr9:26976800-27017800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr9:26977200-27019400	Weak transcription	NH-A	brain
8	chr9:26977800-27026000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr9:26979400-27024000	Weak transcription	Small Intestine	intestine
10	chr9:26982800-27023800	Weak transcription	Lung	lung
11	chr9:26983600-27023800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr9:26985200-27011800	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr9:26985200-27011800	Weak transcription	Colon Smooth Muscle	Colon
14	chr9:26985200-27015800	Weak transcription	Brain Angular Gyrus	brain
15	chr9:26985200-27016200	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr9:26985200-27017400	Weak transcription	Brain Substantia Nigra	brain
17	chr9:26985200-27024000	Weak transcription	Right Ventricle	heart
18	chr9:26985200-27024000	Weak transcription	HSMM	muscle
19	chr9:26985200-27063800	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr9:26985400-27001000	Weak transcription	Brain Anterior Caudate	brain
21	chr9:26985400-27003400	Weak transcription	Duodenum Mucosa	Duodenum
22	chr9:26985400-27004000	Weak transcription	Rectal Smooth Muscle	rectum
23	chr9:26985400-27012200	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr9:26985400-27012400	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr9:26985400-27013000	Weak transcription	Brain Hippocampus Middle	brain
26	chr9:26985400-27015600	Weak transcription	Primary T cells from cord blood	blood
27	chr9:26985400-27015800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr9:26985400-27017400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr9:26985400-27017400	Weak transcription	Brain Cingulate Gyrus	brain
30	chr9:26985400-27017800	Weak transcription	Fetal Thymus	thymus
31	chr9:26985400-27024000	Weak transcription	A549	lung
32	chr9:26985600-27024400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr9:26985800-27018800	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr9:26986000-27012200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr9:26986600-27004000	Weak transcription	Colonic Mucosa	Colon
36	chr9:26986800-27016000	Weak transcription	Ovary	ovary
37	chr9:26987200-27017200	Weak transcription	Fetal Muscle Trunk	muscle
38	chr9:26987200-27023800	Weak transcription	HSMMtube	muscle
39	chr9:26987400-27019000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr9:26987400-27024000	Weak transcription	Aorta	Aorta
41	chr9:26987600-27012000	Weak transcription	Stomach Smooth Muscle	stomach
42	chr9:26987800-27016000	Weak transcription	Adipose Nuclei	Adipose
43	chr9:26990800-27013000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr9:26991200-27003600	Weak transcription	Fetal Kidney	kidney
45	chr9:26991400-27017800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr9:26991600-27016200	Weak transcription	Primary hematopoietic stem cells	blood
47	chr9:26991600-27017400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr9:26991800-27058000	Weak transcription	NHDF-Ad	bronchial
49	chr9:26992000-27010200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr9:26992800-27017200	Weak transcription	Fetal Stomach	stomach

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