Variant report

Variant	rs2288031
Chromosome Location	chr16:71902142-71902143
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:71901013..71902699-chr16:71913700..71915306,2	MCF-7	breast:
2	chr16:71896567..71899503-chr16:71901717..71904863,3	K562	blood:
3	chr16:71841575..71843307-chr16:71901661..71904621,2	K562	blood:
4	chr16:71884375..71886145-chr16:71899843..71902432,2	K562	blood:

Variant related genes	Relation type
ENSG00000102984	Chromatin interaction
ENSG00000166747	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs11075908	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11075911	0.87[EUR][1000 genomes]
rs11648353	0.86[EUR][1000 genomes]
rs11648530	0.87[EUR][1000 genomes]
rs11649672	0.93[EUR][1000 genomes]
rs11859903	1.00[JPT][hapmap]
rs12102548	1.00[CEU][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12444829	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12447045	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12449139	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12599192	0.89[EUR][1000 genomes]
rs12921084	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12926041	0.90[EUR][1000 genomes]
rs12926300	0.89[EUR][1000 genomes]
rs12930744	0.86[EUR][1000 genomes]
rs12935795	0.86[EUR][1000 genomes]
rs13329779	0.96[EUR][1000 genomes]
rs1834034	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1834035	0.95[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs1981874	1.00[CEU][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2008675	0.84[EUR][1000 genomes]
rs2018384	0.93[EUR][1000 genomes]
rs2288029	0.96[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2335709	0.92[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs2335710	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2335711	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2335712	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2335713	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2335714	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2335715	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28697038	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2878492	0.87[EUR][1000 genomes]
rs3794692	0.94[EUR][1000 genomes]
rs4788446	0.82[EUR][1000 genomes]
rs4788447	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4788449	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4788450	0.88[YRI][hapmap]
rs4788562	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4788563	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4788564	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4788566	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4788570	1.00[CEU][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4788571	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4788573	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4788576	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4788579	0.89[YRI][hapmap]
rs4788581	0.93[EUR][1000 genomes]
rs4788582	0.88[EUR][1000 genomes]
rs4788584	0.87[EUR][1000 genomes]
rs4788585	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes]
rs62053803	0.87[EUR][1000 genomes]
rs6499533	1.00[JPT][hapmap]
rs6499542	0.91[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6499545	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6499551	0.95[EUR][1000 genomes]
rs6499552	0.96[EUR][1000 genomes]
rs6558	1.00[JPT][hapmap]
rs7184437	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7184486	0.92[CEU][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7186890	1.00[JPT][hapmap]
rs7187129	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7193731	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7194858	1.00[JPT][hapmap]
rs7204708	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs7205154	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8044342	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8046859	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8050488	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8050651	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8051038	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8054111	0.84[EUR][1000 genomes]
rs8054175	0.84[EUR][1000 genomes]
rs8054403	0.83[EUR][1000 genomes]
rs8057124	0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs8058118	0.94[EUR][1000 genomes]
rs8059053	0.87[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs8062946	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8063324	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs8063403	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9302631	0.96[EUR][1000 genomes]
rs9302632	0.95[EUR][1000 genomes]
rs9806882	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9806905	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs9888748	0.86[EUR][1000 genomes]
rs9889011	0.86[EUR][1000 genomes]
rs9921412	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs9932922	0.90[EUR][1000 genomes]
rs9934803	0.89[EUR][1000 genomes]
rs9934812	0.89[EUR][1000 genomes]
rs9937936	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3347477	chr16:71555148-71985177	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv948468	chr16:71727571-72651914	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2288031	PSMD7	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71881000-71902200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr16:71881200-71916600	Weak transcription	Small Intestine	intestine
3	chr16:71881800-71904600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr16:71881800-71914400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr16:71881800-71914600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr16:71882000-71903800	Strong transcription	Brain Germinal Matrix	brain
7	chr16:71882000-71915600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr16:71882400-71902400	Strong transcription	Fetal Stomach	stomach
9	chr16:71882400-71914600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr16:71885200-71912800	Weak transcription	NHDF-Ad	bronchial
11	chr16:71885600-71916600	Weak transcription	Stomach Mucosa	stomach
12	chr16:71886400-71904200	Strong transcription	Fetal Muscle Trunk	muscle
13	chr16:71886400-71904600	Strong transcription	Fetal Brain Female	brain
14	chr16:71888000-71914800	Weak transcription	HUVEC	blood vessel
15	chr16:71888000-71916400	Weak transcription	NHEK	skin
16	chr16:71888200-71910600	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr16:71888400-71903000	Weak transcription	K562	blood
18	chr16:71888600-71903800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr16:71889200-71904000	Strong transcription	Primary T cells from cord blood	blood
20	chr16:71890200-71913000	Weak transcription	Osteobl	bone
21	chr16:71891000-71914000	Strong transcription	Primary B cells from peripheral blood	blood
22	chr16:71891400-71905400	Strong transcription	Fetal Lung	lung
23	chr16:71891400-71906600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr16:71892000-71903400	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr16:71892600-71904400	Strong transcription	Primary T helper cells PMA-I stimulated	--
26	chr16:71892800-71902200	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr16:71892800-71902600	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr16:71893000-71905200	Strong transcription	Brain Anterior Caudate	brain
29	chr16:71893200-71904200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr16:71893200-71911000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr16:71893400-71902400	Strong transcription	Duodenum Smooth Muscle	Duodenum
32	chr16:71893400-71904800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr16:71893600-71902400	Strong transcription	Stomach Smooth Muscle	stomach
34	chr16:71893600-71902600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr16:71894000-71902400	Strong transcription	Ovary	ovary
36	chr16:71894400-71904000	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr16:71894600-71904200	Strong transcription	Fetal Intestine Large	intestine
38	chr16:71894600-71916800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr16:71895000-71904400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr16:71895600-71902200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr16:71895800-71916400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr16:71896000-71903200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr16:71896000-71913400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr16:71896000-71913800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr16:71896800-71916600	Weak transcription	NHLF	lung
46	chr16:71897600-71902400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr16:71897600-71904200	Strong transcription	Primary B cells from cord blood	blood
48	chr16:71897800-71915600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr16:71898000-71902200	Strong transcription	Aorta	Aorta
50	chr16:71898000-71902200	Strong transcription	GM12878-XiMat	blood

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