Variant report

Variant	rs3788994
Chromosome Location	chr6:25587836-25587837
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1028318	0.80[GIH][hapmap]
rs1028319	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10498728	1.00[YRI][hapmap]
rs10946785	0.80[GIH][hapmap]
rs11969981	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs12526321	0.87[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12528159	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17252870	0.83[CEU][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17253044	0.83[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17322552	1.00[YRI][hapmap]
rs17491869	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2064128	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs214055	0.93[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2294344	1.00[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs301393	0.83[CEU][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs35676593	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3804118	0.80[GIH][hapmap]
rs3804133	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3923725	1.00[YRI][hapmap]
rs4140641	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs4419666	1.00[YRI][hapmap]
rs447724	0.80[ASN][1000 genomes]
rs4711085	0.89[EUR][1000 genomes]
rs4712950	1.00[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs57141743	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61340952	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6903765	0.80[GIH][hapmap]
rs6908390	0.80[GIH][hapmap]
rs72839025	0.82[ASN][1000 genomes]
rs742130	0.98[AMR][1000 genomes];0.94[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	esv3423198	chr6:25585523-25588371	Weak transcription Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3788994	KAAG1	cis	parietal	SCAN
rs3788994	HIST1H3E	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	chr6:25522400-25588600	Weak transcription	HMEC	breast
4	chr6:25538600-25592800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr6:25541600-25612000	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr6:25544000-25593600	Weak transcription	Fetal Lung	lung
7	chr6:25547200-25600600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr6:25556200-25618000	Weak transcription	Primary B cells from cord blood	blood
9	chr6:25557200-25591400	Weak transcription	Ovary	ovary
10	chr6:25572000-25622200	Weak transcription	HSMMtube	muscle
11	chr6:25574200-25594200	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr6:25577000-25590600	Weak transcription	Brain Angular Gyrus	brain
13	chr6:25577200-25592000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr6:25577200-25594200	Weak transcription	Brain Substantia Nigra	brain
15	chr6:25577200-25603400	Weak transcription	Fetal Brain Female	brain
16	chr6:25577200-25624800	Weak transcription	Adipose Nuclei	Adipose
17	chr6:25577600-25597200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr6:25579200-25604600	Weak transcription	Fetal Brain Male	brain
19	chr6:25579600-25588600	Weak transcription	Primary hematopoietic stem cells	blood
20	chr6:25579600-25593200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr6:25580000-25588400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr6:25580000-25590000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr6:25580200-25597800	Weak transcription	Hela-S3	cervix
24	chr6:25580200-25599000	Weak transcription	NHEK	skin
25	chr6:25580400-25592600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr6:25580600-25608600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr6:25580600-25610200	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr6:25580800-25599600	Weak transcription	Small Intestine	intestine
29	chr6:25581200-25622800	Weak transcription	Colonic Mucosa	Colon
30	chr6:25582000-25594400	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr6:25582000-25611400	Weak transcription	Brain Anterior Caudate	brain
32	chr6:25582000-25626800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr6:25582400-25622200	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr6:25582600-25590400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr6:25582800-25594400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr6:25583200-25600600	Weak transcription	Placenta	Placenta
37	chr6:25583400-25592000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr6:25583600-25588000	Weak transcription	Duodenum Mucosa	Duodenum
39	chr6:25583600-25588600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr6:25583600-25590200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr6:25583600-25598600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr6:25583600-25623200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr6:25583800-25591600	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr6:25583800-25623200	Weak transcription	Esophagus	oesophagus
45	chr6:25584400-25597400	Weak transcription	NHDF-Ad	bronchial
46	chr6:25584600-25591400	Weak transcription	Fetal Intestine Small	intestine
47	chr6:25584800-25591400	Weak transcription	Aorta	Aorta
48	chr6:25585000-25627000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr6:25585200-25588400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr6:25585200-25588600	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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