Variant report

Variant	rs6580109
Chromosome Location	chr5:154073339-154073340
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:154070363..154074948-chr5:154077094..154079891,5	MCF-7	breast:
2	chr5:154072065..154073573-chr5:154131263..154133221,2	MCF-7	breast:
3	chr5:154061423..154063859-chr5:154072276..154076586,3	K562	blood:
4	chr5:154071071..154073621-chr5:154134950..154138665,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LARP1-1	chr5:154070884-154073825	NONHSAT104708

Variant related genes	Relation type
ENSG00000155506	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10039709	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10051493	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1972618	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3893695	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4958382	0.82[AMR][1000 genomes]
rs4958387	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4958759	0.82[AMR][1000 genomes]
rs6580102	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6580104	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6580108	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6580110	0.81[EUR][1000 genomes]
rs6580111	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6868098	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs749777	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7710331	0.81[ASN][1000 genomes]
rs7721183	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7736062	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9324791	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9324792	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs965235	0.82[AMR][1000 genomes]

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:154071200-154076200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr5:154071400-154077200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr5:154071400-154093400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr5:154071600-154073400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr5:154071600-154076000	Weak transcription	Fetal Intestine Large	intestine
6	chr5:154071600-154076200	Weak transcription	Fetal Intestine Small	intestine
7	chr5:154071800-154076000	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr5:154072200-154076000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr5:154072200-154076200	Weak transcription	K562	blood
10	chr5:154072200-154080600	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr5:154072200-154080600	Weak transcription	Stomach Mucosa	stomach
12	chr5:154072200-154081000	Weak transcription	Left Ventricle	heart
13	chr5:154072200-154082800	Weak transcription	Psoas Muscle	Psoas
14	chr5:154072200-154092600	Weak transcription	Adipose Nuclei	Adipose
15	chr5:154072400-154075600	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr5:154072400-154075600	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr5:154072400-154075600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr5:154072400-154075800	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr5:154072400-154075800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr5:154072400-154076000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr5:154072400-154076000	Weak transcription	Fetal Heart	heart
22	chr5:154072400-154076800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr5:154072400-154076800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr5:154072400-154076800	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr5:154072400-154077400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr5:154072400-154078200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr5:154072400-154091800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr5:154072600-154075800	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr5:154072600-154076400	Weak transcription	Osteobl	bone
30	chr5:154072600-154076800	Weak transcription	NHDF-Ad	bronchial
31	chr5:154072800-154076800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr5:154072800-154077000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr5:154073000-154075600	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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