Variant report

Variant	rs7042447
Chromosome Location	chr9:26894478-26894479
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:26894459-26894611	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:26891080..26895841-chr9:26945501..26948974,8	K562	blood:
2	chr9:26891080..26894676-chr9:26945695..26949113,9	K562	blood:
3	chr9:26890425..26894629-chr9:26953159..26958312,6	K562	blood:
4	chr9:26892381..26894407-chr9:26894414..26897617,3	MCF-7	breast:
5	chr9:26892948..26894662-chr9:26974221..26975842,2	K562	blood:
6	chr9:26889862..26894629-chr9:26953159..26958871,9	K562	blood:

No data

Variant related genes	Relation type
RN7SL100P	TF binding region
CAAP1	TF binding region
ENSG00000137055	Chromatin interaction
ENSG00000120159	Chromatin interaction
ENSG00000234676	Chromatin interaction
ENSG00000096872	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10738762	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10757634	0.80[ASN][1000 genomes]
rs10757635	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10757636	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10812479	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10812482	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10812487	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10812488	0.89[CEU][hapmap];0.83[CHB][hapmap];0.88[JPT][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10812494	0.81[JPT][hapmap]
rs10812500	0.83[CEU][hapmap]
rs10812503	0.85[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10812504	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10812507	0.86[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10812508	0.81[ASN][1000 genomes]
rs10812509	0.80[JPT][hapmap]
rs10812518	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs10967548	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10967549	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10967551	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10967556	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10967586	0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs10967594	0.83[CEU][hapmap]
rs10967645	0.89[CHB][hapmap]
rs10967652	0.86[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	0.83[CEU][hapmap]
rs12337896	0.83[CHB][hapmap]
rs12342005	0.89[CEU][hapmap]
rs12345197	0.82[AMR][1000 genomes]
rs1336337	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs1541144	0.86[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs16910895	0.84[CEU][hapmap]
rs17833941	0.81[JPT][hapmap]
rs1819539	0.84[CHB][hapmap]
rs2184438	0.81[ASN][1000 genomes]
rs2225720	0.84[CHB][hapmap]
rs3737226	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs3739547	0.80[JPT][hapmap];0.82[ASN][1000 genomes]
rs3739548	0.83[ASN][1000 genomes]
rs3739550	0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs3758218	0.85[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs4316229	0.82[AMR][1000 genomes]
rs4413873	0.86[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4621911	0.94[CHB][hapmap];0.95[JPT][hapmap]
rs59159685	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62544398	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6475944	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6475945	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]
rs6475946	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6475947	1.00[CEU][hapmap];0.84[JPT][hapmap];0.87[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6475948	0.83[CEU][hapmap]
rs6475954	0.94[CHB][hapmap];0.95[JPT][hapmap]
rs7018585	0.86[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs7019034	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs7020010	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs7032756	0.94[CEU][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7033238	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7034478	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7034670	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7035292	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7038218	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7040505	0.89[CHB][hapmap]
rs7040516	0.84[CEU][hapmap]
rs7042133	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7849248	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs7856462	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7857466	0.81[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs7857481	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7857669	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs7860542	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7863476	0.94[CEU][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7868158	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7870787	0.89[CHB][hapmap];0.85[JPT][hapmap]
rs7871668	0.94[CHB][hapmap];0.95[JPT][hapmap]
rs7872496	0.90[JPT][hapmap]
rs7873073	0.80[CHB][hapmap];0.80[JPT][hapmap];0.80[ASN][1000 genomes]
rs7875068	0.86[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[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
rs7042447	IFT74	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:99 , 50 per page) page: 1 2

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	chr9:26893400-26896200	Weak transcription	Brain Angular Gyrus	brain
11	chr9:26893400-26896200	Weak transcription	Brain Hippocampus Middle	brain
12	chr9:26893400-26896200	Weak transcription	Brain Substantia Nigra	brain
13	chr9:26893400-26901000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr9:26893400-26901000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr9:26893400-26901200	Weak transcription	Gastric	stomach
16	chr9:26893400-26903200	Weak transcription	Primary B cells from cord blood	blood
17	chr9:26893400-26904000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr9:26893400-26904000	Weak transcription	HUVEC	blood vessel
19	chr9:26893400-26904400	Weak transcription	Fetal Brain Male	brain
20	chr9:26893400-26904600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr9:26893400-26904600	Weak transcription	NH-A	brain
22	chr9:26893400-26904800	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr9:26893400-26905200	Weak transcription	Colon Smooth Muscle	Colon
24	chr9:26893400-26905200	Weak transcription	Fetal Muscle Trunk	muscle
25	chr9:26893400-26905400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr9:26893400-26905400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr9:26893400-26905400	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr9:26893400-26905400	Weak transcription	NHDF-Ad	bronchial
29	chr9:26893400-26905600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr9:26893400-26905800	Weak transcription	Fetal Stomach	stomach
31	chr9:26893400-26914800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr9:26893400-26916000	Weak transcription	Fetal Lung	lung
33	chr9:26893400-26916800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr9:26893400-26925000	Weak transcription	Stomach Mucosa	stomach
35	chr9:26893400-26936400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr9:26893400-26936400	Weak transcription	Psoas Muscle	Psoas
37	chr9:26893600-26894600	Weak transcription	Fetal Muscle Leg	muscle
38	chr9:26893600-26894800	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr9:26893600-26896200	Weak transcription	Brain Anterior Caudate	brain
40	chr9:26893600-26896200	Weak transcription	Brain Cingulate Gyrus	brain
41	chr9:26893600-26900600	Weak transcription	HSMM	muscle
42	chr9:26893600-26900800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr9:26893600-26901000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr9:26893600-26901200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr9:26893600-26901200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr9:26893600-26903000	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr9:26893600-26903000	Weak transcription	A549	lung
48	chr9:26893600-26903200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr9:26893600-26903600	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr9:26893600-26903800	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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