Variant report

Variant	rs7518300
Chromosome Location	chr1:172438264-172438265
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:172419066..172420955-chr1:172437059..172439364,2	MCF-7	breast:
2	chr1:172435073..172439525-chr1:172499726..172502954,7	MCF-7	breast:
3	chr1:172420111..172423084-chr1:172435694..172439908,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000094975	Chromatin interaction
ENSG00000180999	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1009802	1.00[CHD][hapmap]
rs1129942	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16844417	1.00[CHD][hapmap]
rs17278379	1.00[CHD][hapmap]
rs17369123	0.84[CEU][hapmap]
rs2001130	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2001132	1.00[CEU][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2018244	0.94[AMR][1000 genomes]
rs2213738	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2901655	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3948765	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4244193	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4244194	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4916187	1.00[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4916260	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4916261	1.00[CEU][hapmap];0.92[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6659116	0.89[EUR][1000 genomes]
rs6660798	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6689291	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs739249	1.00[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7515895	1.00[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.92[MEX][hapmap];0.89[EUR][1000 genomes]
rs7522692	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7538417	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7544376	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7551242	1.00[CHD][hapmap]
rs9425328	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425330	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425620	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7518300	GPA33	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172435400-172439000	Enhancers	HepG2	liver
2	chr1:172435400-172439200	Enhancers	Placenta Amnion	Placenta Amnion
3	chr1:172435600-172439200	Weak transcription	Left Ventricle	heart
4	chr1:172435800-172441800	Weak transcription	K562	blood
5	chr1:172436400-172440200	Weak transcription	Right Atrium	heart
6	chr1:172436800-172438800	Weak transcription	Fetal Intestine Small	intestine
7	chr1:172436800-172439000	Weak transcription	Pancreas	Pancrea
8	chr1:172436800-172444200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr1:172437000-172439400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr1:172437000-172440800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr1:172437000-172441200	Weak transcription	NHEK	skin
12	chr1:172437000-172441600	Weak transcription	HMEC	breast
13	chr1:172437000-172444400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr1:172437400-172438400	Weak transcription	Fetal Intestine Large	intestine
15	chr1:172437800-172439000	Weak transcription	A549	lung
16	chr1:172437800-172445400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr1:172438200-172449200	Weak transcription	Fetal Muscle Leg	muscle

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