Variant report

Variant	rs62170159
Chromosome Location	chr2:114589534-114589535
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:114512943..114515625-chr2:114589095..114591354,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ACTR3-3	chr2:114589440-114589975	NONHSAT073844

Variant related genes	Relation type
ENSG00000115084	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10185135	0.82[EUR][1000 genomes]
rs10209659	0.82[EUR][1000 genomes]
rs1028245	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11123214	0.86[ASN][1000 genomes]
rs11675908	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11676646	0.81[EUR][1000 genomes]
rs11685296	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11685654	0.85[ASN][1000 genomes]
rs11691664	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35167892	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4241126	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4292100	0.84[AFR][1000 genomes]
rs4411702	0.82[EUR][1000 genomes]
rs4571059	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4849285	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4849286	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4849287	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4849288	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4849289	0.82[EUR][1000 genomes]
rs4849290	0.82[EUR][1000 genomes]
rs4849291	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4849294	0.85[ASN][1000 genomes]
rs57106417	0.97[AFR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61050591	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62170141	0.82[AFR][1000 genomes]
rs62170143	0.82[AFR][1000 genomes]
rs62170148	0.82[AFR][1000 genomes]
rs62170155	0.97[AFR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62171760	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62171761	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62171768	0.85[ASN][1000 genomes]
rs62171769	0.85[ASN][1000 genomes]
rs72835407	0.82[AFR][1000 genomes]
rs72948684	0.82[EUR][1000 genomes]
rs7579001	0.82[ASN][1000 genomes]
rs9646927	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs62170159	DDX11L2	cis	lung	GTEx
rs62170159	DDX11L2	cis	Esophagus Muscularis	GTEx
rs62170159	DDX11L2	cis	Adipose Subcutaneous	GTEx
rs62170159	RPL23AP7	cis	Artery Aorta	GTEx
rs62170159	RPL23AP7	cis	Heart Left Ventricle	GTEx
rs62170159	RPL23AP7	cis	Whole Blood	GTEx
rs62170159	RPL23AP7	cis	Artery Tibial	GTEx
rs62170159	DDX11L2	cis	Heart Left Ventricle	GTEx
rs62170159	ACTR3	Cis_1M	lymphoblastoid	RTeQTL
rs62170159	DDX11L2	cis	Whole Blood	GTEx
rs62170159	SLC35F5	cis	Thyroid	GTEx

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:114574200-114603600	Weak transcription	Primary B cells from cord blood	blood
2	chr2:114584600-114595600	Weak transcription	HepG2	liver
3	chr2:114584800-114592000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr2:114586400-114591400	Weak transcription	Fetal Intestine Large	intestine
5	chr2:114586400-114601000	Weak transcription	Primary T cells from cord blood	blood
6	chr2:114587800-114590800	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr2:114589000-114591400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr2:114589200-114590000	Enhancers	Placenta	Placenta
9	chr2:114589200-114592000	Weak transcription	HMEC	breast
10	chr2:114589200-114596400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr2:114589200-114600200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr2:114589200-114600200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr2:114589200-114600200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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