Variant report

Variant	rs1028318
Chromosome Location	chr6:25590224-25590225
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10223506	0.87[EUR][1000 genomes]
rs1040419	0.81[EUR][1000 genomes]
rs10447385	0.82[EUR][1000 genomes]
rs10447386	0.82[EUR][1000 genomes]
rs10447387	0.82[EUR][1000 genomes]
rs10447388	0.82[EUR][1000 genomes]
rs10447389	0.82[EUR][1000 genomes]
rs10484591	0.83[EUR][1000 genomes]
rs10946785	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10946786	0.86[EUR][1000 genomes]
rs10946787	0.82[EUR][1000 genomes]
rs11962024	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12183240	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12201186	0.87[EUR][1000 genomes]
rs12524760	0.82[GIH][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs12527646	0.81[EUR][1000 genomes]
rs12528182	0.81[EUR][1000 genomes]
rs12528262	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1321251	0.82[EUR][1000 genomes]
rs1321252	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1406925	0.82[EUR][1000 genomes]
rs1406926	0.82[EUR][1000 genomes]
rs1406927	0.81[EUR][1000 genomes]
rs150551	1.00[CEU][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1569483	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16890878	0.82[EUR][1000 genomes]
rs16890900	0.81[EUR][1000 genomes]
rs1853049	0.82[EUR][1000 genomes]
rs190045	0.85[YRI][hapmap];0.86[AFR][1000 genomes]
rs1980450	0.86[EUR][1000 genomes]
rs1980451	0.86[EUR][1000 genomes]
rs1980452	0.84[EUR][1000 genomes]
rs1997672	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2072842	0.86[EUR][1000 genomes]
rs2072844	0.85[EUR][1000 genomes]
rs2072846	0.84[GIH][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs2077393	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs214055	0.90[YRI][hapmap];0.95[AFR][1000 genomes]
rs214057	0.87[CHD][hapmap];0.85[GIH][hapmap]
rs214065	0.87[CHD][hapmap];0.82[GIH][hapmap]
rs2205933	0.85[EUR][1000 genomes]
rs2208041	0.82[EUR][1000 genomes]
rs2223323	0.85[EUR][1000 genomes]
rs2281070	0.86[EUR][1000 genomes]
rs2281075	0.81[EUR][1000 genomes]
rs3788994	0.80[GIH][hapmap]
rs3804105	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3804106	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3804108	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3804109	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3804118	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]
rs3827500	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4413605	0.87[EUR][1000 genomes]
rs4712948	0.82[EUR][1000 genomes]
rs4712949	0.83[EUR][1000 genomes]
rs4712953	0.86[TSI][hapmap]
rs58262709	0.81[EUR][1000 genomes]
rs59606579	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6456687	0.82[EUR][1000 genomes]
rs6903765	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6903817	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6904044	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6908390	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6935612	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs714563	0.82[EUR][1000 genomes]
rs73397619	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73397648	0.81[EUR][1000 genomes]
rs73397653	0.83[EUR][1000 genomes]
rs73399723	0.82[EUR][1000 genomes]
rs7383628	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs742132	1.00[CEU][hapmap];0.97[GIH][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7754155	0.84[GIH][hapmap];0.88[TSI][hapmap]
rs7761700	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7773087	0.82[EUR][1000 genomes]
rs7774036	0.82[EUR][1000 genomes]
rs876239	0.83[EUR][1000 genomes]
rs909663	0.82[EUR][1000 genomes]
rs909665	0.83[EUR][1000 genomes]
rs9295667	0.86[EUR][1000 genomes]
rs9467538	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9467539	0.86[EUR][1000 genomes]
rs9467541	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9467542	0.86[EUR][1000 genomes]
rs9467552	0.84[GIH][hapmap];0.88[TSI][hapmap]
rs976958	0.81[EUR][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1028318	SCGN	cis	parietal	SCAN
rs1028318	SLC17A1	cis	cerebellum	SCAN
rs1028318	HIST1H3B	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	chr6:25557200-25591400	Weak transcription	Ovary	ovary
9	chr6:25572000-25622200	Weak transcription	HSMMtube	muscle
10	chr6:25574200-25594200	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr6:25577000-25590600	Weak transcription	Brain Angular Gyrus	brain
12	chr6:25577200-25592000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr6:25577200-25594200	Weak transcription	Brain Substantia Nigra	brain
14	chr6:25577200-25603400	Weak transcription	Fetal Brain Female	brain
15	chr6:25577200-25624800	Weak transcription	Adipose Nuclei	Adipose
16	chr6:25577600-25597200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr6:25579200-25604600	Weak transcription	Fetal Brain Male	brain
18	chr6:25579600-25593200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr6:25580200-25597800	Weak transcription	Hela-S3	cervix
20	chr6:25580200-25599000	Weak transcription	NHEK	skin
21	chr6:25580400-25592600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr6:25580600-25608600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr6:25580600-25610200	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr6:25580800-25599600	Weak transcription	Small Intestine	intestine
25	chr6:25581200-25622800	Weak transcription	Colonic Mucosa	Colon
26	chr6:25582000-25594400	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr6:25582000-25611400	Weak transcription	Brain Anterior Caudate	brain
28	chr6:25582000-25626800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr6:25582400-25622200	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr6:25582600-25590400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr6:25582800-25594400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr6:25583200-25600600	Weak transcription	Placenta	Placenta
33	chr6:25583400-25592000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr6:25583600-25598600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr6:25583600-25623200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr6:25583800-25591600	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr6:25583800-25623200	Weak transcription	Esophagus	oesophagus
38	chr6:25584400-25597400	Weak transcription	NHDF-Ad	bronchial
39	chr6:25584600-25591400	Weak transcription	Fetal Intestine Small	intestine
40	chr6:25584800-25591400	Weak transcription	Aorta	Aorta
41	chr6:25585000-25627000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr6:25585200-25592800	Weak transcription	Thymus	Thymus
43	chr6:25585200-25599600	Weak transcription	Fetal Kidney	kidney
44	chr6:25585200-25629400	Weak transcription	Pancreas	Pancrea
45	chr6:25585400-25591400	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr6:25585400-25592200	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr6:25585600-25592800	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr6:25585600-25594000	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr6:25585800-25593000	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr6:25587000-25594000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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