Variant report

Variant	rs2213738
Chromosome Location	chr1:172439443-172439444
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:172423456..172425141-chr1:172439304..172441807,2	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:
4	chr1:172438999..172439573-chr1:172499191..172499779,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000180999	Chromatin interaction
ENSG00000094975	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1009802	1.00[CHD][hapmap];0.83[YRI][hapmap]
rs1129942	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16844417	1.00[CHD][hapmap]
rs17278379	1.00[CHD][hapmap]
rs17369123	0.84[CEU][hapmap]
rs2001130	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2001132	1.00[CEU][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2018244	0.89[AMR][1000 genomes]
rs2901655	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3948765	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4244193	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]
rs4244194	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]
rs4916187	1.00[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.92[MEX][hapmap];0.89[EUR][1000 genomes]
rs4916260	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4916261	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6656400	0.87[ASW][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes]
rs6659116	0.95[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6660798	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6689291	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs739249	1.00[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.92[MEX][hapmap];0.89[EUR][1000 genomes]
rs7515895	1.00[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.84[MEX][hapmap];0.89[EUR][1000 genomes]
rs7518300	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]
rs7522692	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7538417	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7544376	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs7551242	1.00[CHD][hapmap];1.00[YRI][hapmap]
rs9425328	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425330	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425333	0.94[YRI][hapmap];0.81[AFR][1000 genomes]
rs9425620	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9425623	0.93[YRI][hapmap];0.81[AFR][1000 genomes]
rs9425625	0.87[ASW][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2213738	GPA33	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172435800-172441800	Weak transcription	K562	blood
2	chr1:172436400-172440200	Weak transcription	Right Atrium	heart
3	chr1:172436800-172444200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr1:172437000-172440800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr1:172437000-172441200	Weak transcription	NHEK	skin
6	chr1:172437000-172441600	Weak transcription	HMEC	breast
7	chr1:172437000-172444400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:172437800-172445400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr1:172438200-172449200	Weak transcription	Fetal Muscle Leg	muscle
10	chr1:172438400-172439800	Enhancers	Fetal Intestine Large	intestine
11	chr1:172438800-172440000	Enhancers	Primary neutrophils fromperipheralblood	blood
12	chr1:172438800-172440000	Enhancers	Fetal Intestine Small	intestine
13	chr1:172439000-172439600	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr1:172439000-172439600	Enhancers	A549	lung
15	chr1:172439000-172439800	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr1:172439000-172439800	Enhancers	Liver	Liver
17	chr1:172439000-172441000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr1:172439000-172444400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr1:172439200-172439600	Weak transcription	Pancreas	Pancrea
20	chr1:172439200-172439600	Enhancers	Stomach Mucosa	stomach
21	chr1:172439200-172440400	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr1:172439200-172442600	Weak transcription	Placenta	Placenta
23	chr1:172439400-172439600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr1:172439400-172439600	Enhancers	HepG2	liver
25	chr1:172439400-172439600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

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