Variant report

Variant	rs7538417
Chromosome Location	chr1:172441633-172441634
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:172440495..172444630-chr1:172497465..172500697,4	MCF-7	breast:
2	chr1:172435653..172437888-chr1:172440470..172444240,3	MCF-7	breast:
3	chr1:172423456..172425141-chr1:172439304..172441807,2	MCF-7	breast:
4	chr1:172439490..172443248-chr1:172495023..172498932,4	MCF-7	breast:
5	chr1:172435764..172437831-chr1:172441142..172443070,2	K562	blood:
6	chr1:172441394..172443061-chr1:172501494..172503816,2	MCF-7	breast:
7	chr1:172440631..172443212-chr1:172501569..172503673,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000094975	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1009802	1.00[CHD][hapmap]
rs1129942	0.98[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];0.88[YRI][hapmap];0.82[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];0.88[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2901655	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3948765	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4244193	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];0.89[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4244194	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];0.89[YRI][hapmap];0.82[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	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4916261	1.00[CEU][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6659116	0.89[EUR][1000 genomes]
rs6660798	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6689291	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]
rs7518300	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]
rs7522692	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];1.00[YRI][hapmap];0.98[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	0.97[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];0.90[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425620	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7538417	GPA33	cis	parietal	SCAN
rs7538417	VAMP4	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172435800-172441800	Weak transcription	K562	blood
2	chr1:172436800-172444200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr1:172437000-172444400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:172437800-172445400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:172438200-172449200	Weak transcription	Fetal Muscle Leg	muscle
6	chr1:172439000-172444400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:172439200-172442600	Weak transcription	Placenta	Placenta
8	chr1:172439600-172442800	Weak transcription	Stomach Mucosa	stomach
9	chr1:172439800-172442600	Weak transcription	Pancreas	Pancrea
10	chr1:172439800-172443400	Enhancers	HepG2	liver
11	chr1:172440000-172445400	Weak transcription	Fetal Intestine Small	intestine
12	chr1:172440200-172445200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr1:172440400-172442000	Enhancers	Placenta Amnion	Placenta Amnion
14	chr1:172440400-172442600	Enhancers	Primary neutrophils fromperipheralblood	blood
15	chr1:172440800-172442000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr1:172440800-172444200	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr1:172441000-172442200	Enhancers	Monocytes-CD14+_RO01746	blood
18	chr1:172441200-172441800	Enhancers	NHEK	skin
19	chr1:172441400-172442400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr1:172441400-172443200	Enhancers	Primary hematopoietic stem cells	blood
21	chr1:172441400-172443400	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr1:172441400-172443400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr1:172441600-172443000	Enhancers	HMEC	breast

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