Variant report

Variant	rs9425330
Chromosome Location	chr1:172442435-172442436
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:172441688..172443816-chr1:172500587..172502900,2	K562	blood:
2	chr1:172440495..172444630-chr1:172497465..172500697,4	MCF-7	breast:
3	chr1:172435653..172437888-chr1:172440470..172444240,3	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	chr1:172424806..172427327-chr1:172442354..172444546,2	K562	blood:
7	chr1:172441394..172443061-chr1:172501494..172503816,2	MCF-7	breast:
8	chr1:172442195..172443795-chr1:172449989..172451528,2	MCF-7	breast:
9	chr1:172440631..172443212-chr1:172501569..172503673,3	MCF-7	breast:
10	chr1:172442117..172444152-chr1:172447245..172449151,2	MCF-7	breast:

No data

Variant related genes	Relation type
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];0.82[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]
rs2213738	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]
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];0.84[MEX][hapmap];0.98[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];0.85[MEX][hapmap];0.98[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];0.85[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];0.85[MEX][hapmap];0.89[EUR][1000 genomes]
rs7515895	1.00[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.89[EUR][1000 genomes]
rs7518300	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]
rs7522692	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]
rs7538417	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]
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]
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
rs9425330	GPA33	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172436800-172444200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr1:172437000-172444400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:172437800-172445400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:172438200-172449200	Weak transcription	Fetal Muscle Leg	muscle
5	chr1:172439000-172444400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr1:172439200-172442600	Weak transcription	Placenta	Placenta
7	chr1:172439600-172442800	Weak transcription	Stomach Mucosa	stomach
8	chr1:172439800-172442600	Weak transcription	Pancreas	Pancrea
9	chr1:172439800-172443400	Enhancers	HepG2	liver
10	chr1:172440000-172445400	Weak transcription	Fetal Intestine Small	intestine
11	chr1:172440200-172445200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr1:172440400-172442600	Enhancers	Primary neutrophils fromperipheralblood	blood
13	chr1:172440800-172444200	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr1:172441400-172443200	Enhancers	Primary hematopoietic stem cells	blood
15	chr1:172441400-172443400	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr1:172441400-172443400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr1:172441600-172443000	Enhancers	HMEC	breast
18	chr1:172441800-172442800	Weak transcription	NHEK	skin
19	chr1:172441800-172443000	Enhancers	K562	blood
20	chr1:172441800-172443400	Enhancers	Ovary	ovary
21	chr1:172442000-172443400	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr1:172442000-172444400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr1:172442200-172443200	Enhancers	Primary B cells from cord blood	blood
24	chr1:172442200-172443200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr1:172442200-172443200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
26	chr1:172442400-172442800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr1:172442400-172443800	Enhancers	Breast Myoepithelial Primary Cells	Breast

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