Variant report

Variant	rs3747526
Chromosome Location	chr6:25619581-25619582
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:25619323..25622321-chr6:25626739..25629730,2	K562	blood:
2	chr6:25613845..25615932-chr6:25619464..25621877,2	K562	blood:

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1022492	0.86[CEU][hapmap];0.97[GIH][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes]
rs12663643	0.86[EUR][1000 genomes]
rs12665641	0.84[ASW][hapmap];0.88[GIH][hapmap];0.92[TSI][hapmap];0.93[YRI][hapmap]
rs13192159	0.93[CEU][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13201652	0.80[CEU][hapmap]
rs13217586	0.80[CEU][hapmap]
rs1406924	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs16890880	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2049967	0.80[CEU][hapmap];0.81[CHB][hapmap];0.91[GIH][hapmap];0.96[TSI][hapmap]
rs2072845	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2072848	0.83[EUR][1000 genomes]
rs2072849	0.86[CEU][hapmap];0.97[GIH][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs2205935	0.82[CHB][hapmap];0.85[GIH][hapmap];0.92[TSI][hapmap]
rs2272824	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	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3804120	0.85[ASW][hapmap];0.93[CEU][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap];0.87[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3804124	0.86[CEU][hapmap];0.97[GIH][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs3804125	0.86[EUR][1000 genomes]
rs3804126	0.86[CEU][hapmap];0.86[EUR][1000 genomes]
rs3804127	0.86[EUR][1000 genomes]
rs3827505	0.86[CEU][hapmap];0.97[GIH][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs4588684	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6932016	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6935799	0.86[CEU][hapmap];0.93[YRI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6939153	0.85[GIH][hapmap];0.88[TSI][hapmap]
rs7738571	0.86[CEU][hapmap];0.97[GIH][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs7739227	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7740510	0.94[GIH][hapmap]
rs7741329	0.84[CEU][hapmap];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7767930	1.00[ASW][hapmap];0.93[CEU][hapmap];0.97[GIH][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap];0.81[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7776417	0.86[CEU][hapmap]
rs9295665	0.93[CEU][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9348683	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs9356979	0.87[YRI][hapmap]
rs9356980	0.85[EUR][1000 genomes]
rs9356981	0.86[EUR][1000 genomes]
rs9356983	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9358865	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9366625	0.87[YRI][hapmap]
rs9379772	0.86[CEU][hapmap];0.97[GIH][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes]
rs9379776	0.80[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs9393648	0.81[GIH][hapmap]
rs9393649	0.85[EUR][1000 genomes]
rs9393650	0.93[CEU][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs941428	0.81[EUR][1000 genomes];0.92[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
rs3747526	GPX6	cis	parietal	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25572000-25622200	Weak transcription	HSMMtube	muscle
2	chr6:25577200-25624800	Weak transcription	Adipose Nuclei	Adipose
3	chr6:25581200-25622800	Weak transcription	Colonic Mucosa	Colon
4	chr6:25582000-25626800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr6:25582400-25622200	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr6:25583600-25623200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr6:25583800-25623200	Weak transcription	Esophagus	oesophagus
8	chr6:25585000-25627000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr6:25585200-25629400	Weak transcription	Pancreas	Pancrea
10	chr6:25587400-25622400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr6:25589200-25623400	Weak transcription	HMEC	breast
12	chr6:25592400-25625600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr6:25594200-25629200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr6:25594400-25627200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr6:25594600-25627200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr6:25594600-25629600	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr6:25594800-25624600	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr6:25595000-25626800	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr6:25595000-25627000	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr6:25598000-25622800	Weak transcription	Gastric	stomach
21	chr6:25599200-25622800	Weak transcription	Rectal Smooth Muscle	rectum
22	chr6:25601600-25626400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr6:25602800-25623600	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr6:25603800-25624000	Weak transcription	Fetal Kidney	kidney
25	chr6:25606600-25621000	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr6:25607000-25622000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr6:25608000-25621200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr6:25609400-25627000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr6:25610400-25620400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr6:25610400-25624200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr6:25611000-25622800	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr6:25611200-25621000	Weak transcription	Stomach Smooth Muscle	stomach
33	chr6:25611200-25623200	Weak transcription	Lung	lung
34	chr6:25611600-25625200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr6:25611800-25621000	Weak transcription	Fetal Intestine Large	intestine
36	chr6:25611800-25621000	Weak transcription	Fetal Lung	lung
37	chr6:25611800-25623000	Weak transcription	Fetal Thymus	thymus
38	chr6:25612000-25620800	Weak transcription	Thymus	Thymus
39	chr6:25612400-25623600	Weak transcription	Ovary	ovary
40	chr6:25612600-25621200	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr6:25612800-25620800	Weak transcription	Duodenum Mucosa	Duodenum
42	chr6:25612800-25623400	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr6:25612800-25626800	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr6:25613200-25620800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr6:25613200-25624200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr6:25613200-25631000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr6:25613400-25623600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr6:25618000-25620000	Enhancers	Primary B cells from cord blood	blood
49	chr6:25618000-25620200	Enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr6:25618000-25620200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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