Variant report

Variant	rs2747039
Chromosome Location	chr1:94230778-94230779
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:94225633..94227882-chr1:94228603..94231021,2	K562	blood:
2	chr1:94230167..94233599-chr1:94234522..94237747,3	K562	blood:
3	chr1:94230247..94233265-chr1:94234348..94236266,3	K562	blood:

Extended variants
information (count: 61 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10489602	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10489603	0.81[CEU][hapmap]
rs10489604	0.96[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs10782966	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10782967	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11165020	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs11165022	0.83[JPT][hapmap]
rs11165024	0.87[EUR][1000 genomes]
rs11165026	0.83[JPT][hapmap]
rs12027630	0.85[EUR][1000 genomes]
rs12041975	0.83[JPT][hapmap]
rs12122113	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12123957	0.83[EUR][1000 genomes]
rs12134359	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12137687	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12140446	0.96[CEU][hapmap];1.00[JPT][hapmap]
rs12143274	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12143279	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12563731	0.87[EUR][1000 genomes]
rs12565614	0.88[EUR][1000 genomes]
rs12566531	0.87[EUR][1000 genomes]
rs12734571	0.85[EUR][1000 genomes]
rs12739186	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs12745990	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1398798	0.88[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1884018	1.00[CEU][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes]
rs1980083	0.86[CEU][hapmap];0.81[EUR][1000 genomes]
rs2143990	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2143992	0.83[JPT][hapmap]
rs2235971	0.96[CEU][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes]
rs2391315	0.90[CHB][hapmap];0.87[JPT][hapmap]
rs2391322	0.88[CEU][hapmap];0.95[JPT][hapmap]
rs2747041	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2747043	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2747045	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2747050	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2818160	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2818162	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2818164	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2818169	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3000471	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3747965	0.96[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs4075523	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4141736	0.85[EUR][1000 genomes]
rs4141737	0.96[CEU][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes]
rs4240955	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4240956	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4314890	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4350209	0.83[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4847253	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4847255	0.81[EUR][1000 genomes]
rs4847256	0.82[CEU][hapmap]
rs4847264	0.83[JPT][hapmap]
rs6663218	0.82[JPT][hapmap]
rs6664719	0.96[CEU][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes]
rs6681265	0.82[JPT][hapmap]
rs6685747	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7364910	0.88[EUR][1000 genomes]
rs743111	0.82[JPT][hapmap]
rs8179391	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs871854	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2747039	RP11-488P3.1	cis	Thyroid	GTEx
rs2747039	RP11-488P3.1	cis	Adipose Subcutaneous	GTEx
rs2747039	RP11-488P3.1	cis	Heart Left Ventricle	GTEx
rs2747039	RP11-488P3.1	cis	Skin Sun Exposed Lower leg	GTEx
rs2747039	RP11-488P3.1	cis	Stomach	GTEx
rs2747039	RP11-488P3.1	cis	Esophagus Muscularis	GTEx
rs2747039	RP11-488P3.1	cis	lung	GTEx
rs2747039	RP11-488P3.1	cis	Muscle Skeletal	GTEx
rs2747039	RP11-488P3.1	cis	Nerve Tibial	GTEx
rs2747039	RP11-488P3.1	cis	Artery Tibial	GTEx

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94219800-94231600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:94220000-94254200	Weak transcription	Aorta	Aorta
3	chr1:94223000-94237000	Weak transcription	NHEK	skin
4	chr1:94225000-94231800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr1:94225000-94233600	Weak transcription	Right Atrium	heart
6	chr1:94225400-94231600	Weak transcription	Thymus	Thymus
7	chr1:94225600-94233600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr1:94225600-94233800	Weak transcription	Fetal Lung	lung
9	chr1:94227000-94231800	Weak transcription	HepG2	liver
10	chr1:94227200-94233600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr1:94228200-94233800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr1:94228400-94231400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr1:94229400-94234600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr1:94229600-94231600	Weak transcription	Placenta	Placenta
15	chr1:94229800-94233600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:94229800-94234200	Weak transcription	Pancreas	Pancrea
17	chr1:94230200-94230800	Genic enhancers	HMEC	breast
18	chr1:94230200-94231600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr1:94230400-94230800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr1:94230400-94233200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr1:94230600-94230800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr1:94230600-94230800	Enhancers	Fetal Stomach	stomach
23	chr1:94230600-94232000	Weak transcription	Fetal Muscle Leg	muscle
24	chr1:94230600-94233600	Weak transcription	Lung	lung

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