Variant report

Variant	rs2480777
Chromosome Location	chr1:10597551-10597552
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10864459	0.85[GIH][hapmap]
rs11121587	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1188526	0.82[CEU][hapmap];0.82[CHB][hapmap]
rs12028449	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12375	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1411402	0.90[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17035305	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2026792	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2056417	0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.88[LWK][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2150038	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2480782	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2480784	0.90[CHB][hapmap];0.92[JPT][hapmap]
rs2480785	0.90[EUR][1000 genomes]
rs2483677	0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2506880	0.88[EUR][1000 genomes]
rs2506889	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2506892	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2506896	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2506901	0.82[CEU][hapmap]
rs2781230	0.82[CEU][hapmap];0.93[GIH][hapmap]
rs2847344	0.86[CEU][hapmap];0.87[EUR][1000 genomes]
rs34575776	0.97[EUR][1000 genomes]
rs4846235	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs585870	0.82[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap]
rs589400	0.82[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap]
rs596537	0.81[CEU][hapmap];0.82[CHB][hapmap]
rs607941	0.82[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap]
rs616402	0.91[CEU][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes]
rs616488	0.97[GIH][hapmap]
rs617728	0.90[EUR][1000 genomes]
rs620405	0.81[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.87[TSI][hapmap]
rs622623	0.82[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.87[TSI][hapmap]
rs636291	0.80[GIH][hapmap]
rs648324	0.82[CEU][hapmap];0.82[CHB][hapmap]
rs648399	0.82[CEU][hapmap];0.82[CHB][hapmap]
rs660725	0.81[CEU][hapmap];0.82[CHB][hapmap]
rs662064	0.82[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.87[TSI][hapmap]
rs6687430	0.88[CHD][hapmap];0.86[JPT][hapmap]
rs668805	0.82[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap]
rs669701	0.82[CEU][hapmap];0.82[CHB][hapmap]
rs67488812	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9430149	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817370	chr1:10305470-10697150	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1008021	chr1:10363794-10802633	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv1003498	chr1:10445928-10607351	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv998731	chr1:10464176-10607351	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv2521	chr1:10553530-10598171	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv545395	chr1:10584672-10613660	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2480777	SLC2A5	cis	parietal	SCAN
rs2480777	AADACL3	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10572200-10598600	Weak transcription	Brain Anterior Caudate	brain
2	chr1:10577000-10603600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr1:10579400-10610200	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr1:10584800-10603800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr1:10585200-10603600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr1:10585200-10603800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr1:10588400-10598200	Weak transcription	Pancreas	Pancrea
8	chr1:10588800-10599200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr1:10589000-10600000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr1:10589200-10598600	Weak transcription	Brain Cingulate Gyrus	brain
11	chr1:10589400-10664800	Weak transcription	Aorta	Aorta
12	chr1:10590200-10602800	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr1:10590200-10605200	Weak transcription	NHDF-Ad	bronchial
14	chr1:10590600-10599400	Weak transcription	GM12878-XiMat	blood
15	chr1:10590800-10598600	Weak transcription	Right Atrium	heart
16	chr1:10590800-10599800	Weak transcription	Right Ventricle	heart
17	chr1:10590800-10601000	Weak transcription	A549	lung
18	chr1:10591000-10600200	Weak transcription	HUVEC	blood vessel
19	chr1:10591000-10639400	Weak transcription	Hela-S3	cervix
20	chr1:10591200-10599200	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr1:10591200-10599200	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr1:10591200-10601000	Weak transcription	Placenta	Placenta
23	chr1:10591200-10601400	Weak transcription	Colonic Mucosa	Colon
24	chr1:10591400-10599600	Weak transcription	Fetal Kidney	kidney
25	chr1:10591400-10599600	Weak transcription	Ovary	ovary
26	chr1:10591400-10609000	Weak transcription	Small Intestine	intestine
27	chr1:10591400-10629200	Weak transcription	Primary hematopoietic stem cells	blood
28	chr1:10591600-10599800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:10591600-10616000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr1:10592000-10598600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr1:10592000-10598600	Weak transcription	Stomach Smooth Muscle	stomach
32	chr1:10592000-10599200	Weak transcription	HSMM	muscle
33	chr1:10592000-10599600	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr1:10592200-10599200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr1:10592200-10599200	Weak transcription	NH-A	brain
36	chr1:10592200-10615800	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr1:10592400-10598600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr1:10592600-10597600	Weak transcription	Psoas Muscle	Psoas
39	chr1:10592600-10598200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr1:10592600-10598600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr1:10592600-10599200	Weak transcription	Fetal Lung	lung
42	chr1:10592800-10598000	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr1:10592800-10599800	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr1:10593000-10598000	Weak transcription	Fetal Heart	heart
45	chr1:10593000-10598200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr1:10593000-10598600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr1:10593000-10599200	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr1:10593000-10599400	Weak transcription	Rectal Smooth Muscle	rectum
49	chr1:10593000-10599800	Weak transcription	Brain Angular Gyrus	brain
50	chr1:10593000-10603800	Weak transcription	Fetal Brain Female	brain

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