Variant report

Variant	rs2617617
Chromosome Location	chr5:127455008-127455009
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	chr5:127421269..127422991-chr5:127453839..127456834,2	MCF-7	breast:

Extended variants
information (count: 17 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1112956	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11948128	0.93[ASN][1000 genomes]
rs17764730	0.82[ASN][1000 genomes]
rs1993878	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2250127	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2409110	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2568928	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34576922	0.82[ASN][1000 genomes]
rs3749748	0.81[ASN][1000 genomes]
rs6860245	0.82[ASN][1000 genomes]
rs6888037	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6889311	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7734927	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs790154	0.84[EUR][1000 genomes]
rs790155	0.84[EUR][1000 genomes]
rs9327468	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3422179	chr5:127450653-127456051	Weak transcription ZNF genes & repeats Strong transcription Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2617617	FLJ33630	Cis_1M	lymphoblastoid	RTeQTL
rs2617617	CTC-228N24.3	cis	Skin Sun Exposed Lower leg	GTEx
rs2617617	CTC-228N24.3	cis	Muscle Skeletal	GTEx
rs2617617	CTC-228N24.3	cis	Thyroid	GTEx

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:127421600-127466800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr5:127423600-127494000	Weak transcription	K562	blood
3	chr5:127441200-127536800	Weak transcription	Colonic Mucosa	Colon
4	chr5:127441400-127457400	Weak transcription	Stomach Mucosa	stomach
5	chr5:127442400-127525000	Weak transcription	Right Ventricle	heart
6	chr5:127443000-127457200	Weak transcription	Pancreas	Pancrea
7	chr5:127443000-127467000	Weak transcription	Esophagus	oesophagus
8	chr5:127443800-127459800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr5:127444400-127457600	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr5:127445200-127456600	Weak transcription	Spleen	Spleen
11	chr5:127445200-127466800	Weak transcription	Gastric	stomach
12	chr5:127445200-127480200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr5:127445400-127491800	Weak transcription	Psoas Muscle	Psoas
14	chr5:127447000-127525000	Weak transcription	Fetal Brain Male	brain
15	chr5:127447800-127466600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr5:127448400-127458600	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr5:127449000-127457400	Weak transcription	Placenta	Placenta
18	chr5:127451000-127466800	Weak transcription	Thymus	Thymus
19	chr5:127451200-127465800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr5:127451200-127465800	Weak transcription	Fetal Intestine Small	intestine
21	chr5:127451400-127490600	Weak transcription	Aorta	Aorta
22	chr5:127451600-127488200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr5:127451800-127466800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr5:127451800-127471800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr5:127451800-127488600	Weak transcription	Osteobl	bone
26	chr5:127451800-127490400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr5:127452000-127457200	Weak transcription	Left Ventricle	heart
28	chr5:127452000-127457200	Weak transcription	NHEK	skin
29	chr5:127452000-127457400	Weak transcription	HMEC	breast
30	chr5:127452000-127465800	Weak transcription	Fetal Stomach	stomach
31	chr5:127452000-127466800	Weak transcription	Stomach Smooth Muscle	stomach
32	chr5:127452000-127467000	Weak transcription	Lung	lung
33	chr5:127452000-127473200	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr5:127452000-127477200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr5:127452000-127477600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr5:127452000-127490400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr5:127452200-127457600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr5:127452600-127459600	Weak transcription	Ovary	ovary
39	chr5:127452600-127472400	Weak transcription	Rectal Smooth Muscle	rectum
40	chr5:127453000-127459800	Weak transcription	HSMMtube	muscle
41	chr5:127453000-127463600	Weak transcription	HUVEC	blood vessel
42	chr5:127453000-127473800	Weak transcription	Colon Smooth Muscle	Colon
43	chr5:127453200-127455200	ZNF genes & repeats	Fetal Brain Female	brain
44	chr5:127453200-127473000	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr5:127453400-127455400	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
46	chr5:127453600-127493800	Weak transcription	Liver	Liver
47	chr5:127453600-127525400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr5:127453800-127455200	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
49	chr5:127453800-127455400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr5:127454000-127455200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain

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