Variant report

Variant	rs1040285
Chromosome Location	chr6:109583186-109583187
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:109575810..109578673-chr6:109582353..109584012,2	MCF-7	breast:
2	chr6:109580166..109583539-chr6:109585250..109587755,3	MCF-7	breast:
3	chr6:109577168..109578931-chr6:109582878..109584392,2	K562	blood:

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1113665	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1113666	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs11153163	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13216168	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1341269	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1815038	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2090887	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4590308	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4945828	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4946951	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4946952	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6919557	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7755798	0.83[CEU][hapmap]
rs7775345	0.87[CEU][hapmap]
rs9320279	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs9374067	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9374070	0.89[ASW][hapmap]
rs9384703	0.89[ASW][hapmap]
rs9384704	0.84[ASW][hapmap]
rs9386778	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9386784	0.89[ASW][hapmap]
rs9398190	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9398191	0.89[ASW][hapmap]
rs949881	0.89[ASW][hapmap]
rs949882	0.89[ASW][hapmap]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1040285	PRDM1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109564000-109590400	Weak transcription	Psoas Muscle	Psoas
2	chr6:109572800-109590400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr6:109572800-109595200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr6:109573200-109589800	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr6:109573600-109590200	Weak transcription	Gastric	stomach
6	chr6:109574600-109583400	Weak transcription	Placenta	Placenta
7	chr6:109575800-109589200	Weak transcription	Pancreas	Pancrea
8	chr6:109577200-109583400	Weak transcription	Fetal Kidney	kidney
9	chr6:109579000-109583200	Weak transcription	Fetal Muscle Trunk	muscle
10	chr6:109579600-109584200	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr6:109580600-109583400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr6:109581000-109583600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr6:109581600-109583200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr6:109581800-109583800	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr6:109581800-109588800	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr6:109582200-109583600	Enhancers	Fetal Stomach	stomach
17	chr6:109582400-109583400	Weak transcription	HSMM	muscle
18	chr6:109582600-109583200	Enhancers	Rectal Smooth Muscle	rectum
19	chr6:109582600-109583600	Enhancers	Fetal Lung	lung
20	chr6:109582800-109583400	Enhancers	Adipose Nuclei	Adipose
21	chr6:109582800-109583600	Enhancers	Colon Smooth Muscle	Colon
22	chr6:109582800-109584000	Enhancers	Ovary	ovary
23	chr6:109583000-109583600	Enhancers	Fetal Muscle Leg	muscle
24	chr6:109583000-109583600	Enhancers	Stomach Smooth Muscle	stomach
25	chr6:109583000-109587600	Strong transcription	HepG2	liver

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