Variant report

Variant	rs3804120
Chromosome Location	chr6:25592547-25592548
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1022492	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10434845	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs12663643	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12665641	0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap]
rs13192159	1.00[CEU][hapmap];0.83[CHB][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13201652	0.87[CEU][hapmap];0.82[JPT][hapmap]
rs13203202	0.82[JPT][hapmap]
rs13217586	0.87[CEU][hapmap]
rs1406924	0.82[AMR][1000 genomes]
rs2049967	0.87[CEU][hapmap];0.88[GIH][hapmap];0.87[TSI][hapmap]
rs2072845	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2072848	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2072849	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs212934	0.83[CHB][hapmap]
rs2205935	0.82[GIH][hapmap];0.82[JPT][hapmap];0.84[TSI][hapmap]
rs2272824	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]
rs2328879	0.82[JPT][hapmap]
rs3747526	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]
rs3788992	0.93[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3804122	0.81[ASN][1000 genomes]
rs3804123	0.83[CHB][hapmap];0.84[CHD][hapmap];0.81[ASN][1000 genomes]
rs3804124	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3804125	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3804126	0.93[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3804127	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3827505	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4588684	0.85[AMR][1000 genomes]
rs6935799	0.93[CEU][hapmap];0.90[CHB][hapmap];0.93[YRI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6939153	0.82[GIH][hapmap];0.82[JPT][hapmap]
rs7738571	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7739227	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7740510	0.91[GIH][hapmap]
rs7741329	0.92[CEU][hapmap]
rs7767930	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7776417	0.93[CEU][hapmap];0.95[CHB][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9295665	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9348683	0.93[CEU][hapmap];0.95[CHB][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9356979	0.91[CHB][hapmap];0.87[YRI][hapmap]
rs9356980	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9356981	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9356983	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9358860	0.80[ASN][1000 genomes]
rs9366625	0.91[CHB][hapmap];0.87[YRI][hapmap]
rs9379772	0.93[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9379776	0.87[CEU][hapmap];0.86[JPT][hapmap]
rs9379777	0.82[JPT][hapmap]
rs9393648	0.91[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.88[TSI][hapmap]
rs9393649	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9393650	1.00[CEU][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs941428	0.82[EUR][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
rs3804120	GPX6	cis	parietal	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25471600-25597200	Weak transcription	Gastric	stomach
2	chr6:25516800-25606400	Weak transcription	Lung	lung
3	chr6:25538600-25592800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr6:25541600-25612000	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr6:25544000-25593600	Weak transcription	Fetal Lung	lung
6	chr6:25547200-25600600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr6:25556200-25618000	Weak transcription	Primary B cells from cord blood	blood
8	chr6:25572000-25622200	Weak transcription	HSMMtube	muscle
9	chr6:25574200-25594200	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr6:25577200-25594200	Weak transcription	Brain Substantia Nigra	brain
11	chr6:25577200-25603400	Weak transcription	Fetal Brain Female	brain
12	chr6:25577200-25624800	Weak transcription	Adipose Nuclei	Adipose
13	chr6:25577600-25597200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr6:25579200-25604600	Weak transcription	Fetal Brain Male	brain
15	chr6:25579600-25593200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr6:25580200-25597800	Weak transcription	Hela-S3	cervix
17	chr6:25580200-25599000	Weak transcription	NHEK	skin
18	chr6:25580400-25592600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr6:25580600-25608600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr6:25580600-25610200	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr6:25580800-25599600	Weak transcription	Small Intestine	intestine
22	chr6:25581200-25622800	Weak transcription	Colonic Mucosa	Colon
23	chr6:25582000-25594400	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr6:25582000-25611400	Weak transcription	Brain Anterior Caudate	brain
25	chr6:25582000-25626800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr6:25582400-25622200	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr6:25582800-25594400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr6:25583200-25600600	Weak transcription	Placenta	Placenta
29	chr6:25583600-25598600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr6:25583600-25623200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr6:25583800-25623200	Weak transcription	Esophagus	oesophagus
32	chr6:25584400-25597400	Weak transcription	NHDF-Ad	bronchial
33	chr6:25585000-25627000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr6:25585200-25592800	Weak transcription	Thymus	Thymus
35	chr6:25585200-25599600	Weak transcription	Fetal Kidney	kidney
36	chr6:25585200-25629400	Weak transcription	Pancreas	Pancrea
37	chr6:25585600-25592800	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr6:25585600-25594000	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr6:25585800-25593000	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr6:25587000-25594000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr6:25587200-25592800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr6:25587400-25622400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr6:25587600-25599200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr6:25587800-25598200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr6:25588000-25596200	Strong transcription	Duodenum Mucosa	Duodenum
46	chr6:25588600-25593600	Weak transcription	Fetal Stomach	stomach
47	chr6:25589000-25603000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr6:25589000-25604600	Weak transcription	Fetal Thymus	thymus
49	chr6:25589200-25593000	Weak transcription	Primary hematopoietic stem cells	blood
50	chr6:25589200-25623400	Weak transcription	HMEC	breast

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