Variant report

Variant	rs7849248
Chromosome Location	chr9:26979027-26979028
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 93 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10738762	1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs10757635	1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs10757636	0.89[ASN][1000 genomes]
rs10812488	0.87[CHB][hapmap]
rs10812494	0.84[JPT][hapmap]
rs10812502	0.85[ASN][1000 genomes]
rs10812503	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs10812504	0.91[ASN][1000 genomes]
rs10812506	0.86[ASN][1000 genomes]
rs10812507	1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs10812508	0.82[ASN][1000 genomes]
rs10812509	0.89[JPT][hapmap]
rs10812510	0.90[JPT][hapmap]
rs10812517	0.90[JPT][hapmap]
rs10812518	0.94[CHB][hapmap];0.92[CHD][hapmap];0.89[JPT][hapmap]
rs10967621	0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs10967622	0.84[ASN][1000 genomes]
rs10967623	0.84[ASN][1000 genomes]
rs10967627	0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs10967629	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10967630	0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs10967632	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10967633	0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs10967635	0.86[CHD][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs10967636	0.86[ASN][1000 genomes]
rs10967645	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.87[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10967648	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10967649	0.88[CHD][hapmap];0.95[JPT][hapmap]
rs10967650	0.90[JPT][hapmap]
rs10967652	0.94[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs10967661	0.88[CHD][hapmap]
rs10967678	0.89[JPT][hapmap]
rs10967679	0.94[CHB][hapmap];0.90[JPT][hapmap]
rs10967688	0.84[JPT][hapmap]
rs11534184	0.84[ASN][1000 genomes]
rs11555693	0.86[ASN][1000 genomes]
rs11562224	0.83[ASN][1000 genomes]
rs12235490	0.86[ASN][1000 genomes]
rs12236850	0.86[CHD][hapmap]
rs12237867	0.85[ASN][1000 genomes]
rs12337896	0.88[CHB][hapmap];0.97[CHD][hapmap]
rs1336337	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs1537639	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1541144	1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs1577328	0.82[CHB][hapmap]
rs17833941	0.89[JPT][hapmap]
rs1819539	0.88[CHB][hapmap]
rs1970187	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2184438	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2184439	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2225720	0.88[CHB][hapmap]
rs3737226	0.84[JPT][hapmap]
rs3739544	0.90[JPT][hapmap];0.85[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs3739547	0.88[CHD][hapmap];0.84[JPT][hapmap]
rs3739550	0.84[JPT][hapmap]
rs3758218	1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs4413873	0.94[CHB][hapmap];0.82[JPT][hapmap]
rs4621911	0.94[CHB][hapmap];0.90[JPT][hapmap]
rs55827505	0.84[ASN][1000 genomes]
rs55870543	0.82[ASN][1000 genomes]
rs57450012	0.84[ASN][1000 genomes]
rs60841248	0.86[ASN][1000 genomes]
rs6475945	0.84[JPT][hapmap]
rs6475954	0.94[CHB][hapmap];0.90[JPT][hapmap]
rs7018585	1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs7019034	0.84[JPT][hapmap]
rs7020010	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7034115	0.88[ASN][1000 genomes]
rs7034478	0.91[ASN][1000 genomes]
rs7034888	0.86[ASN][1000 genomes]
rs7034899	0.86[ASN][1000 genomes]
rs7035447	0.86[CHD][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs7038218	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs7040505	0.88[CHB][hapmap]
rs7042447	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs7856462	0.88[CHB][hapmap];0.84[JPT][hapmap]
rs7857447	0.90[JPT][hapmap]
rs7857466	0.84[JPT][hapmap]
rs7857669	0.94[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap]
rs7860542	1.00[CHB][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs7863476	0.85[CHD][hapmap];0.84[JPT][hapmap]
rs7865952	0.84[ASN][1000 genomes]
rs7868158	0.84[JPT][hapmap]
rs7870787	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7871668	0.94[CHB][hapmap];0.90[JPT][hapmap]
rs7873073	0.90[CHD][hapmap];0.84[JPT][hapmap]
rs7874940	0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs7875068	1.00[CHB][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs7875171	0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs9644870	0.88[CHD][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7849248	IFT74	cis	lymphoblastoid	seeQTL
rs7849248	IFT74	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:26957000-26980800	Weak transcription	Lung	lung
2	chr9:26957000-26983200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr9:26957000-26984400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr9:26957000-27024000	Weak transcription	Esophagus	oesophagus
5	chr9:26957200-26980800	Weak transcription	Fetal Intestine Large	intestine
6	chr9:26957200-26980800	Weak transcription	Fetal Stomach	stomach
7	chr9:26957200-26982600	Weak transcription	Fetal Muscle Leg	muscle
8	chr9:26957200-26982600	Weak transcription	Left Ventricle	heart
9	chr9:26957200-26983200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr9:26957200-26983200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr9:26957200-26984400	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr9:26957200-26984400	Weak transcription	Primary B cells from peripheral blood	blood
13	chr9:26957200-26984600	Weak transcription	Fetal Muscle Trunk	muscle
14	chr9:26957200-26984800	Weak transcription	Primary B cells from cord blood	blood
15	chr9:26957200-26984800	Weak transcription	Fetal Thymus	thymus
16	chr9:26957200-27026600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr9:26957200-27040000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr9:26957400-26980800	Weak transcription	Duodenum Mucosa	Duodenum
19	chr9:26957400-26982800	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr9:26957400-26983200	Weak transcription	Brain Anterior Caudate	brain
21	chr9:26957400-26983400	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr9:26957400-26984600	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr9:26957600-26979400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr9:26957600-26982800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr9:26957600-26983200	Weak transcription	Fetal Kidney	kidney
26	chr9:26957600-26983400	Weak transcription	Brain Angular Gyrus	brain
27	chr9:26957600-26984800	Weak transcription	Brain Hippocampus Middle	brain
28	chr9:26957800-26984600	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr9:26958600-26981000	Weak transcription	Ovary	ovary
30	chr9:26962200-26981600	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr9:26962200-26986400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr9:26962400-26984600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr9:26962400-26985000	Weak transcription	Brain Substantia Nigra	brain
34	chr9:26962600-26984600	Weak transcription	HSMM	muscle
35	chr9:26963800-26983200	Weak transcription	Primary hematopoietic stem cells	blood
36	chr9:26966400-26984600	Weak transcription	Fetal Brain Male	brain
37	chr9:26969000-26991200	Weak transcription	NHDF-Ad	bronchial
38	chr9:26969600-26986600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr9:26970400-26982600	Weak transcription	Fetal Lung	lung
40	chr9:26970400-26983200	Weak transcription	Primary T cells from cord blood	blood
41	chr9:26970400-26984200	Weak transcription	Dnd41	blood
42	chr9:26970800-26990000	Weak transcription	Spleen	Spleen
43	chr9:26971000-26980800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr9:26971000-26983200	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr9:26971600-26982600	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr9:26972000-26981400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr9:26972200-26986200	Weak transcription	Pancreas	Pancrea
48	chr9:26972200-26995000	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr9:26972800-26986800	Weak transcription	Aorta	Aorta
50	chr9:26972800-26990600	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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