Variant report

Variant	rs17247566
Chromosome Location	chr6:24450404-24450405
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10946700	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10946701	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12194966	0.85[TSI][hapmap];0.81[ASN][1000 genomes]
rs12198188	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12524609	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13191455	1.00[ASW][hapmap];0.82[MEX][hapmap];0.86[YRI][hapmap]
rs13192752	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs13205577	0.88[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13205780	1.00[ASW][hapmap];0.82[MEX][hapmap];0.86[YRI][hapmap];0.81[ASN][1000 genomes]
rs34089102	0.88[AMR][1000 genomes]
rs3846833	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60830931	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62400468	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6922313	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6922631	0.88[CEU][hapmap];0.85[YRI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs71544274	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7762593	0.86[YRI][hapmap];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7762901	1.00[ASW][hapmap];0.88[CEU][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7766620	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs807508	1.00[JPT][hapmap]
rs807521	1.00[JPT][hapmap]
rs807525	1.00[JPT][hapmap]
rs807534	1.00[JPT][hapmap]
rs807535	1.00[JPT][hapmap]
rs807545	1.00[JPT][hapmap]
rs9295624	0.88[CEU][hapmap];0.94[MEX][hapmap];0.85[TSI][hapmap];0.85[YRI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9461010	0.93[CEU][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9461011	0.87[CEU][hapmap];0.92[YRI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9461012	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9461014	0.86[YRI][hapmap];0.81[ASN][1000 genomes]
rs9461015	1.00[ASW][hapmap];0.82[MEX][hapmap];0.86[YRI][hapmap];0.81[ASN][1000 genomes]
rs9467148	0.81[ASN][1000 genomes]
rs9467157	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9467158	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9467160	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9467161	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9467166	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9467168	0.86[YRI][hapmap];0.81[ASN][1000 genomes]
rs9467170	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9467171	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467172	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026638	chr6:24347972-24475300	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	9 gene(s)	inside rSNPs	diseases
2	esv2763542	chr6:24445131-24520637	Strong transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17247566	SLC17A4	cis	parietal	SCAN
rs17247566	HIST1H2AH	cis	cerebellum	SCAN
rs17247566	HIST1H3C	cis	parietal	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24417400-24451800	Strong transcription	Liver	Liver
2	chr6:24421200-24459600	Weak transcription	Spleen	Spleen
3	chr6:24424000-24456600	Weak transcription	Ovary	ovary
4	chr6:24427600-24456800	Weak transcription	Lung	lung
5	chr6:24427800-24467000	Weak transcription	Brain Germinal Matrix	brain
6	chr6:24429000-24494200	Weak transcription	Primary B cells from cord blood	blood
7	chr6:24429200-24455600	Weak transcription	Brain Angular Gyrus	brain
8	chr6:24429400-24483800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr6:24429600-24455000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr6:24432600-24463800	Weak transcription	Fetal Intestine Small	intestine
11	chr6:24433600-24451600	Weak transcription	Adipose Nuclei	Adipose
12	chr6:24437600-24455400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr6:24437800-24450600	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr6:24437800-24459600	Weak transcription	Left Ventricle	heart
15	chr6:24438000-24464000	Weak transcription	Pancreas	Pancrea
16	chr6:24438200-24455600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr6:24438400-24483200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr6:24438600-24459800	Weak transcription	Fetal Stomach	stomach
19	chr6:24438800-24469200	Weak transcription	Brain Cingulate Gyrus	brain
20	chr6:24440400-24452000	Weak transcription	Primary T cells from cord blood	blood
21	chr6:24441400-24452000	Weak transcription	Thymus	Thymus
22	chr6:24442000-24452000	Weak transcription	Fetal Thymus	thymus
23	chr6:24444000-24458200	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr6:24446400-24451600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr6:24446400-24451800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr6:24447200-24470200	Weak transcription	Aorta	Aorta
27	chr6:24447400-24490400	Weak transcription	Brain Anterior Caudate	brain
28	chr6:24448200-24466200	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr6:24448400-24452000	Weak transcription	K562	blood
30	chr6:24448400-24458000	Weak transcription	Stomach Smooth Muscle	stomach
31	chr6:24448800-24488000	Weak transcription	Fetal Muscle Leg	muscle
32	chr6:24449400-24451600	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr6:24450000-24452000	Weak transcription	Gastric	stomach
34	chr6:24450200-24459400	Weak transcription	Esophagus	oesophagus
35	chr6:24450400-24451800	Weak transcription	Primary neutrophils fromperipheralblood	blood

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