Variant report

Variant	rs62542706
Chromosome Location	chr9:27054957-27054958
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	chr9:27044880..27046633-chr9:27052693..27055070,2	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10511795	0.86[AFR][1000 genomes]
rs10511797	0.86[AFR][1000 genomes]
rs1161603	0.81[ASN][1000 genomes]
rs1541145	0.86[AFR][1000 genomes]
rs1591356	0.90[ASN][1000 genomes]
rs17694631	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17756179	0.86[AFR][1000 genomes]
rs17756299	0.91[AFR][1000 genomes]
rs2991949	0.81[ASN][1000 genomes]
rs3429	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57770546	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60130669	0.86[AFR][1000 genomes]
rs62542663	0.86[AFR][1000 genomes]
rs62542665	0.86[AFR][1000 genomes]
rs62542667	0.91[AFR][1000 genomes]
rs62542669	0.91[AFR][1000 genomes]
rs62542670	0.91[AFR][1000 genomes]
rs62542672	0.95[AFR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62542704	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62542705	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62542707	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62542708	0.91[AFR][1000 genomes]
rs62546685	0.86[AFR][1000 genomes]
rs625630	0.81[ASN][1000 genomes]
rs627339	0.81[ASN][1000 genomes]
rs639826	0.81[ASN][1000 genomes]
rs7038875	0.86[AFR][1000 genomes]
rs73436012	0.86[AFR][1000 genomes]
rs73436044	0.86[AFR][1000 genomes]
rs73436047	0.91[AFR][1000 genomes]
rs73438223	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73438278	0.86[AFR][1000 genomes]
rs73438282	0.86[AFR][1000 genomes]
rs73438302	0.86[AFR][1000 genomes]
rs73440204	0.86[AFR][1000 genomes]
rs73440205	0.86[AFR][1000 genomes]
rs73440214	0.86[AFR][1000 genomes]
rs73440217	0.86[AFR][1000 genomes]
rs73440218	0.81[AFR][1000 genomes]
rs7865596	0.86[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
4	nsv466334	chr9:27028947-27098940	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
5	nsv613944	chr9:27028947-27098940	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62542706	IFT74	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:26985200-27063800	Weak transcription	Primary T helper cells PMA-I stimulated	--
2	chr9:26991800-27058000	Weak transcription	NHDF-Ad	bronchial
3	chr9:27009800-27070000	Weak transcription	Psoas Muscle	Psoas
4	chr9:27014400-27060800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr9:27014400-27068200	Weak transcription	Fetal Heart	heart
6	chr9:27018400-27065200	Weak transcription	Osteobl	bone
7	chr9:27019200-27061800	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr9:27024400-27082600	Weak transcription	Gastric	stomach
9	chr9:27024600-27056400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr9:27024600-27058800	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr9:27024600-27059600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr9:27024600-27061000	Weak transcription	Dnd41	blood
13	chr9:27024600-27061400	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr9:27024600-27061800	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr9:27024600-27064400	Weak transcription	Colonic Mucosa	Colon
16	chr9:27024600-27075800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr9:27024600-27078600	Weak transcription	Aorta	Aorta
18	chr9:27024600-27079000	Weak transcription	Pancreas	Pancrea
19	chr9:27024600-27082400	Weak transcription	Primary T cells from cord blood	blood
20	chr9:27024600-27083400	Weak transcription	Left Ventricle	heart
21	chr9:27024600-27085000	Weak transcription	Brain Cingulate Gyrus	brain
22	chr9:27024600-27086800	Weak transcription	Right Ventricle	heart
23	chr9:27024800-27056800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr9:27024800-27058200	Weak transcription	Fetal Brain Male	brain
25	chr9:27024800-27060000	Weak transcription	Fetal Kidney	kidney
26	chr9:27024800-27094800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr9:27025200-27056000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr9:27025200-27064800	Weak transcription	Fetal Brain Female	brain
29	chr9:27025200-27078000	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr9:27025400-27063600	Weak transcription	Brain Substantia Nigra	brain
31	chr9:27025400-27066800	Weak transcription	Brain Anterior Caudate	brain
32	chr9:27025400-27075600	Weak transcription	Fetal Muscle Trunk	muscle
33	chr9:27037000-27069600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr9:27038000-27085000	Weak transcription	Brain Hippocampus Middle	brain
35	chr9:27038200-27061000	Weak transcription	Fetal Intestine Large	intestine
36	chr9:27038200-27065400	Weak transcription	Primary B cells from peripheral blood	blood
37	chr9:27042400-27058600	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr9:27042400-27063600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr9:27046000-27061000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr9:27046200-27058400	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr9:27046600-27068000	Weak transcription	Rectal Smooth Muscle	rectum
42	chr9:27047400-27058400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr9:27047600-27057400	Weak transcription	Brain Germinal Matrix	brain
44	chr9:27048800-27076200	Weak transcription	Stomach Smooth Muscle	stomach
45	chr9:27049000-27065800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr9:27049200-27056000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr9:27049200-27056000	Weak transcription	Liver	Liver
48	chr9:27049200-27056800	Weak transcription	Duodenum Mucosa	Duodenum
49	chr9:27049200-27057000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr9:27049200-27057800	Weak transcription	Rectal Mucosa Donor 29	rectum

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