Variant report

Variant	rs7860542
Chromosome Location	chr9:26899130-26899131
allele	A/C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:26894759..26896593-chr9:26898391..26900808,2	K562	blood:
2	chr9:26891285..26894088-chr9:26896175..26900385,5	K562	blood:
3	chr9:26889735..26894428-chr9:26898446..26903207,7	K562	blood:
4	chr9:26898930..26900769-chr9:26941051..26942769,2	MCF-7	breast:
5	chr9:26894775..26896593-chr9:26898921..26900808,2	K562	blood:
6	chr9:26899122..26901033-chr9:26907283..26909966,2	K562	blood:

Variant related genes	Relation type
ENSG00000240306	Chromatin interaction
ENSG00000120159	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10738762	0.86[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10757634	0.80[ASN][1000 genomes]
rs10757635	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10757636	0.89[ASN][1000 genomes]
rs10812488	0.85[CEU][hapmap];0.83[CHB][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs10812494	0.81[JPT][hapmap]
rs10812500	0.85[CEU][hapmap]
rs10812503	0.81[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs10812504	0.86[ASN][1000 genomes]
rs10812507	0.82[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs10812508	0.81[ASN][1000 genomes]
rs10812509	0.80[JPT][hapmap]
rs10812518	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs10967586	0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs10967594	0.85[CEU][hapmap]
rs10967629	0.82[ASN][1000 genomes]
rs10967632	0.82[ASN][1000 genomes]
rs10967645	0.90[CHB][hapmap]
rs10967652	0.82[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs10967679	0.94[CHB][hapmap];0.95[JPT][hapmap]
rs12004732	0.85[CEU][hapmap]
rs12337896	0.83[CHB][hapmap]
rs12342005	0.85[CEU][hapmap]
rs1336337	0.83[CHB][hapmap];0.81[ASN][1000 genomes]
rs1541144	0.82[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs16910895	0.86[CEU][hapmap]
rs17833941	0.81[JPT][hapmap]
rs1819539	0.84[CHB][hapmap]
rs2184438	0.84[ASN][1000 genomes]
rs2184439	0.82[ASN][1000 genomes]
rs2225720	0.84[CHB][hapmap]
rs3737226	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs3739547	0.80[JPT][hapmap]
rs3739550	0.81[JPT][hapmap]
rs3758218	0.81[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs4413873	0.82[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap]
rs4621911	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs59159685	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6475945	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs6475947	1.00[CEU][hapmap];0.84[JPT][hapmap]
rs6475948	0.85[CEU][hapmap]
rs6475954	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs7018585	0.82[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs7019034	0.81[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs7020010	0.95[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs7032756	1.00[CEU][hapmap]
rs7033238	0.81[AMR][1000 genomes]
rs7034115	0.83[ASN][1000 genomes]
rs7034478	0.86[ASN][1000 genomes]
rs7035755	0.85[CEU][hapmap]
rs7038218	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7039400	0.85[CEU][hapmap]
rs7040505	0.90[CHB][hapmap]
rs7040516	0.86[CEU][hapmap]
rs7042133	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7042447	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7045881	0.85[CEU][hapmap]
rs7849248	1.00[CHB][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs7856462	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7857466	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs7857669	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs7863476	0.93[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs7868158	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs7870787	0.89[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs7871668	0.94[CHB][hapmap];0.95[JPT][hapmap]
rs7872496	0.90[JPT][hapmap]
rs7873073	0.80[CHB][hapmap];0.80[JPT][hapmap]
rs7875068	0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]

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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7860542	IFT74	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:26892800-26916200	Weak transcription	Small Intestine	intestine
2	chr9:26893000-26905600	Weak transcription	Lung	lung
3	chr9:26893000-26916000	Weak transcription	Left Ventricle	heart
4	chr9:26893000-26916000	Weak transcription	Pancreas	Pancrea
5	chr9:26893000-26916200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr9:26893000-26922600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr9:26893000-26924200	Weak transcription	Esophagus	oesophagus
8	chr9:26893200-26905600	Weak transcription	Ovary	ovary
9	chr9:26893200-26923200	Weak transcription	Right Ventricle	heart
10	chr9:26893400-26901000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr9:26893400-26901000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr9:26893400-26901200	Weak transcription	Gastric	stomach
13	chr9:26893400-26903200	Weak transcription	Primary B cells from cord blood	blood
14	chr9:26893400-26904000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr9:26893400-26904000	Weak transcription	HUVEC	blood vessel
16	chr9:26893400-26904400	Weak transcription	Fetal Brain Male	brain
17	chr9:26893400-26904600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr9:26893400-26904600	Weak transcription	NH-A	brain
19	chr9:26893400-26904800	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr9:26893400-26905200	Weak transcription	Colon Smooth Muscle	Colon
21	chr9:26893400-26905200	Weak transcription	Fetal Muscle Trunk	muscle
22	chr9:26893400-26905400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr9:26893400-26905400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr9:26893400-26905400	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr9:26893400-26905400	Weak transcription	NHDF-Ad	bronchial
26	chr9:26893400-26905600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr9:26893400-26905800	Weak transcription	Fetal Stomach	stomach
28	chr9:26893400-26914800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr9:26893400-26916000	Weak transcription	Fetal Lung	lung
30	chr9:26893400-26916800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr9:26893400-26925000	Weak transcription	Stomach Mucosa	stomach
32	chr9:26893400-26936400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr9:26893400-26936400	Weak transcription	Psoas Muscle	Psoas
34	chr9:26893600-26900600	Weak transcription	HSMM	muscle
35	chr9:26893600-26900800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr9:26893600-26901000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr9:26893600-26901200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr9:26893600-26901200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr9:26893600-26903000	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr9:26893600-26903000	Weak transcription	A549	lung
41	chr9:26893600-26903200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr9:26893600-26903600	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr9:26893600-26903800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr9:26893600-26904000	Weak transcription	Fetal Thymus	thymus
45	chr9:26893600-26904200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr9:26893600-26904200	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr9:26893600-26904600	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr9:26893600-26904800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr9:26893600-26905200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr9:26893600-26905200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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