Variant report

Variant	rs3804118
Chromosome Location	chr6:25592651-25592652
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 110 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs1012898	0.89[JPT][hapmap]
rs10223506	0.86[EUR][1000 genomes]
rs1028318	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1040417	0.89[JPT][hapmap]
rs1040418	0.89[JPT][hapmap]
rs10447385	0.81[EUR][1000 genomes]
rs10447386	0.81[EUR][1000 genomes]
rs10447387	0.81[EUR][1000 genomes]
rs10447388	0.81[EUR][1000 genomes]
rs10447389	0.81[EUR][1000 genomes]
rs10456324	0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs10484591	0.89[JPT][hapmap];0.82[EUR][1000 genomes]
rs10946785	1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10946786	0.85[EUR][1000 genomes]
rs10946787	0.81[EUR][1000 genomes]
rs10946789	0.84[JPT][hapmap]
rs11962024	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12183240	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12201186	0.86[EUR][1000 genomes]
rs12524760	0.82[GIH][hapmap];0.84[JPT][hapmap];0.88[TSI][hapmap];0.80[EUR][1000 genomes]
rs12525376	0.84[JPT][hapmap]
rs12527646	0.80[EUR][1000 genomes]
rs12528182	0.84[JPT][hapmap];0.80[EUR][1000 genomes]
rs12528262	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12529390	0.84[JPT][hapmap]
rs1321251	0.81[EUR][1000 genomes]
rs1321252	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1406925	0.81[EUR][1000 genomes]
rs1406926	0.81[EUR][1000 genomes]
rs1406927	0.86[JPT][hapmap]
rs150551	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1569483	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16890878	0.81[EUR][1000 genomes]
rs1853049	0.81[EUR][1000 genomes]
rs1883260	0.89[JPT][hapmap]
rs1883261	0.89[JPT][hapmap]
rs190045	0.85[YRI][hapmap];0.85[AFR][1000 genomes]
rs1980450	0.85[EUR][1000 genomes]
rs1980451	0.85[EUR][1000 genomes]
rs1980452	0.83[EUR][1000 genomes]
rs1997672	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2064126	0.83[JPT][hapmap]
rs2064127	0.84[JPT][hapmap]
rs2072842	0.85[EUR][1000 genomes]
rs2072844	0.84[EUR][1000 genomes]
rs2072846	0.84[GIH][hapmap];0.84[JPT][hapmap];0.88[TSI][hapmap]
rs2072847	0.84[JPT][hapmap]
rs2072851	0.84[JPT][hapmap]
rs2077393	1.00[CEU][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs214055	0.90[YRI][hapmap];0.96[AFR][1000 genomes]
rs214057	0.85[GIH][hapmap]
rs214065	0.82[GIH][hapmap]
rs2205933	0.84[EUR][1000 genomes]
rs2208041	0.81[EUR][1000 genomes]
rs2223323	0.84[EUR][1000 genomes]
rs2281070	0.85[EUR][1000 genomes]
rs2281075	0.80[EUR][1000 genomes]
rs2294345	0.89[JPT][hapmap]
rs2328890	0.84[JPT][hapmap]
rs3788994	0.80[GIH][hapmap]
rs3804105	1.00[CEU][hapmap];0.84[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3804106	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3804108	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3804109	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3804115	0.89[JPT][hapmap]
rs3804116	0.88[JPT][hapmap]
rs3804117	0.89[JPT][hapmap]
rs3804121	0.81[CHB][hapmap]
rs3827500	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4140640	0.84[JPT][hapmap]
rs4413605	0.86[EUR][1000 genomes]
rs4711088	0.89[JPT][hapmap]
rs4712948	0.81[EUR][1000 genomes]
rs4712949	0.82[EUR][1000 genomes]
rs4712952	0.89[JPT][hapmap]
rs4712953	0.84[JPT][hapmap];0.86[TSI][hapmap]
rs4712954	0.84[JPT][hapmap]
rs58262709	0.80[EUR][1000 genomes]
rs59606579	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6456687	0.81[EUR][1000 genomes]
rs6903765	1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6903817	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6904044	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6908390	1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6935612	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs714563	0.81[EUR][1000 genomes]
rs73397619	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73397648	0.80[EUR][1000 genomes]
rs73397653	0.82[EUR][1000 genomes]
rs73399723	0.81[EUR][1000 genomes]
rs7383628	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs742132	1.00[CEU][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7754155	0.84[GIH][hapmap];0.84[JPT][hapmap];0.88[TSI][hapmap]
rs7761700	1.00[CEU][hapmap];0.84[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7766874	0.86[CHB][hapmap]
rs7773087	0.81[EUR][1000 genomes]
rs7774036	0.81[EUR][1000 genomes]
rs7775000	0.84[JPT][hapmap]
rs876239	0.82[EUR][1000 genomes]
rs909663	0.81[EUR][1000 genomes]
rs909665	0.82[EUR][1000 genomes]
rs9295667	0.85[EUR][1000 genomes]
rs9348687	0.90[CHB][hapmap]
rs9467538	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9467539	0.85[EUR][1000 genomes]
rs9467541	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9467542	0.85[EUR][1000 genomes]
rs9467552	0.84[GIH][hapmap];0.84[JPT][hapmap];0.88[TSI][hapmap]
rs976958	0.80[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3804118	HIST1H3E	cis	parietal	SCAN
rs3804118	SCGN	cis	parietal	SCAN
rs3804118	HIST1H3B	cis	cerebellum	SCAN
rs3804118	SLC17A1	cis	cerebellum	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	chr6:25580600-25608600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr6:25580600-25610200	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr6:25580800-25599600	Weak transcription	Small Intestine	intestine
21	chr6:25581200-25622800	Weak transcription	Colonic Mucosa	Colon
22	chr6:25582000-25594400	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr6:25582000-25611400	Weak transcription	Brain Anterior Caudate	brain
24	chr6:25582000-25626800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr6:25582400-25622200	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr6:25582800-25594400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr6:25583200-25600600	Weak transcription	Placenta	Placenta
28	chr6:25583600-25598600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr6:25583600-25623200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr6:25583800-25623200	Weak transcription	Esophagus	oesophagus
31	chr6:25584400-25597400	Weak transcription	NHDF-Ad	bronchial
32	chr6:25585000-25627000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr6:25585200-25592800	Weak transcription	Thymus	Thymus
34	chr6:25585200-25599600	Weak transcription	Fetal Kidney	kidney
35	chr6:25585200-25629400	Weak transcription	Pancreas	Pancrea
36	chr6:25585600-25592800	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr6:25585600-25594000	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr6:25585800-25593000	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr6:25587000-25594000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr6:25587200-25592800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr6:25587400-25622400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr6:25587600-25599200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr6:25587800-25598200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr6:25588000-25596200	Strong transcription	Duodenum Mucosa	Duodenum
45	chr6:25588600-25593600	Weak transcription	Fetal Stomach	stomach
46	chr6:25589000-25603000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr6:25589000-25604600	Weak transcription	Fetal Thymus	thymus
48	chr6:25589200-25593000	Weak transcription	Primary hematopoietic stem cells	blood
49	chr6:25589200-25623400	Weak transcription	HMEC	breast
50	chr6:25589400-25594000	Weak transcription	Fetal Intestine Large	intestine

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