Variant report

Variant	rs2272824
Chromosome Location	chr6:25610615-25610616
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1022492	0.86[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes]
rs12663643	0.89[EUR][1000 genomes]
rs12665641	0.84[ASW][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.92[TSI][hapmap]
rs13192159	0.93[CEU][hapmap];0.90[EUR][1000 genomes]
rs13201652	0.80[CEU][hapmap]
rs13217586	0.80[CEU][hapmap]
rs1406924	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs16890880	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2049967	0.80[CEU][hapmap];0.91[GIH][hapmap];0.88[TSI][hapmap]
rs2072845	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2072848	0.86[EUR][1000 genomes]
rs2072849	0.86[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes]
rs2205935	0.85[GIH][hapmap];0.84[TSI][hapmap]
rs3747526	1.00[ASW][hapmap];0.86[CEU][hapmap];0.85[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];0.92[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3788992	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3804120	0.85[ASW][hapmap];0.93[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3804124	0.86[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes]
rs3804125	0.89[EUR][1000 genomes]
rs3804126	0.86[CEU][hapmap];0.86[CHB][hapmap];0.89[EUR][1000 genomes]
rs3804127	0.89[EUR][1000 genomes]
rs3827505	0.86[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes]
rs4588684	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6932016	0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6935799	0.86[CEU][hapmap];0.89[EUR][1000 genomes]
rs6939153	0.85[GIH][hapmap];0.81[TSI][hapmap]
rs7738571	0.86[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes]
rs7739227	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7740510	0.94[GIH][hapmap]
rs7741329	0.84[CEU][hapmap];0.81[ASN][1000 genomes]
rs7751329	0.90[AFR][1000 genomes]
rs7767930	1.00[ASW][hapmap];0.93[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7776417	0.86[CEU][hapmap];0.82[CHB][hapmap];0.82[EUR][1000 genomes]
rs9295665	0.93[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9348683	0.86[CEU][hapmap];0.82[CHB][hapmap];0.85[EUR][1000 genomes]
rs9356980	0.88[EUR][1000 genomes]
rs9356981	0.89[EUR][1000 genomes]
rs9356983	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9358865	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9379772	0.86[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes]
rs9379776	0.80[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9393648	0.81[CHD][hapmap];0.81[GIH][hapmap];0.81[TSI][hapmap]
rs9393649	0.88[EUR][1000 genomes]
rs9393650	0.93[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs941428	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883488	chr6:25592489-25731691	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2272824	GPX6	cis	parietal	SCAN

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25541600-25612000	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr6:25556200-25618000	Weak transcription	Primary B cells from cord blood	blood
3	chr6:25572000-25622200	Weak transcription	HSMMtube	muscle
4	chr6:25577200-25624800	Weak transcription	Adipose Nuclei	Adipose
5	chr6:25581200-25622800	Weak transcription	Colonic Mucosa	Colon
6	chr6:25582000-25611400	Weak transcription	Brain Anterior Caudate	brain
7	chr6:25582000-25626800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr6:25582400-25622200	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr6:25583600-25623200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr6:25583800-25623200	Weak transcription	Esophagus	oesophagus
11	chr6:25585000-25627000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr6:25585200-25629400	Weak transcription	Pancreas	Pancrea
13	chr6:25587400-25622400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr6:25589200-25623400	Weak transcription	HMEC	breast
15	chr6:25590800-25618000	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr6:25592400-25625600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr6:25593600-25618600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr6:25594200-25629200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr6:25594400-25618200	Weak transcription	Primary hematopoietic stem cells	blood
20	chr6:25594400-25627200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr6:25594600-25627200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr6:25594600-25629600	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr6:25594800-25624600	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr6:25595000-25626800	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr6:25595000-25627000	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr6:25595600-25618000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr6:25597800-25610800	Weak transcription	Left Ventricle	heart
28	chr6:25598000-25622800	Weak transcription	Gastric	stomach
29	chr6:25599200-25622800	Weak transcription	Rectal Smooth Muscle	rectum
30	chr6:25599400-25618600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr6:25600600-25612400	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr6:25601000-25612200	Weak transcription	Placenta	Placenta
33	chr6:25601000-25619400	Weak transcription	Fetal Stomach	stomach
34	chr6:25601200-25612000	Weak transcription	Brain Cingulate Gyrus	brain
35	chr6:25601600-25626400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr6:25602600-25611400	Weak transcription	Fetal Lung	lung
37	chr6:25602800-25623600	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr6:25603400-25617800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr6:25603800-25624000	Weak transcription	Fetal Kidney	kidney
40	chr6:25604600-25612800	Strong transcription	Duodenum Mucosa	Duodenum
41	chr6:25604800-25615000	Strong transcription	Primary T cells from cord blood	blood
42	chr6:25605800-25614400	Weak transcription	Fetal Brain Male	brain
43	chr6:25606000-25617200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr6:25606200-25613800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr6:25606400-25612000	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr6:25606400-25613400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr6:25606600-25621000	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr6:25607000-25622000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr6:25607800-25610800	Weak transcription	Thymus	Thymus
50	chr6:25608000-25611000	Weak transcription	Rectal Mucosa Donor 29	rectum

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