Variant report

Variant	rs2056417
Chromosome Location	chr1:10581658-10581659
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:10581501..10583988-chr1:10587081..10589695,2	MCF-7	breast:
2	chr1:10579090..10582212-chr1:10583289..10585385,3	K562	blood:
3	chr1:10575137..10577327-chr1:10580431..10584030,4	K562	blood:

Extended variants
information (count: 66 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10864459	0.86[CEU][hapmap];0.85[GIH][hapmap];0.87[TSI][hapmap]
rs10864460	0.86[CEU][hapmap]
rs11121587	0.82[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1152739	0.83[EUR][1000 genomes]
rs1188525	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1188526	0.91[CEU][hapmap];0.91[CHB][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12028449	0.86[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12375	0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.88[LWK][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1307489	0.83[CHB][hapmap]
rs1308520	0.83[CHB][hapmap]
rs1411402	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1632108	0.86[EUR][1000 genomes]
rs17035305	0.82[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2026792	0.91[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2150038	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2480777	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]
rs2480782	0.90[CHB][hapmap];0.92[JPT][hapmap]
rs2480784	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2480785	0.98[EUR][1000 genomes]
rs2483677	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2483686	0.83[CHB][hapmap]
rs2506880	0.96[EUR][1000 genomes]
rs2506889	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2506892	0.91[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2506896	0.91[EUR][1000 genomes]
rs2506901	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs2506902	0.90[CEU][hapmap]
rs2781230	0.91[CEU][hapmap];0.93[GIH][hapmap]
rs2781232	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2847337	0.83[CHB][hapmap]
rs2847344	0.95[CEU][hapmap];0.93[EUR][1000 genomes]
rs34575776	0.89[EUR][1000 genomes]
rs4846235	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs585870	0.91[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.84[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs587916	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs589400	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs596537	0.91[CEU][hapmap];0.91[CHB][hapmap];0.84[JPT][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs597438	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs607941	0.91[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.84[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs616402	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs616488	0.97[GIH][hapmap];0.84[TSI][hapmap]
rs617728	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs620405	0.91[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.84[JPT][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs622623	0.91[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.84[JPT][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs636291	0.86[CEU][hapmap];0.80[GIH][hapmap];0.82[TSI][hapmap]
rs648324	0.91[CEU][hapmap];0.91[CHB][hapmap];0.84[JPT][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs648399	0.91[CEU][hapmap];0.91[CHB][hapmap];0.84[JPT][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs652771	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6540933	0.85[EUR][1000 genomes]
rs660725	0.90[CEU][hapmap];0.91[CHB][hapmap];0.84[JPT][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs662064	0.91[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.84[JPT][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6687430	0.87[CHD][hapmap]
rs668805	0.91[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.84[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs669701	0.91[CEU][hapmap];0.91[CHB][hapmap];0.84[JPT][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs67488812	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs683864	0.86[EUR][1000 genomes]
rs685746	0.86[CEU][hapmap]
rs9430149	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757722	chr1:10238070-10582554	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv2758920	chr1:10238070-10582554	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	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
4	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
5	esv2764192	chr1:10383734-10594186	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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

Variant related diseases (count:1)

Disease	PMID	Source
Self-reported allergy	23817569	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2056417	AADACL3	cis	parietal	SCAN
rs2056417	SLC2A5	cis	parietal	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10570800-10595600	Weak transcription	Primary B cells from cord blood	blood
2	chr1:10572000-10590000	Weak transcription	Spleen	Spleen
3	chr1:10572200-10598600	Weak transcription	Brain Anterior Caudate	brain
4	chr1:10572600-10587600	Weak transcription	Hela-S3	cervix
5	chr1:10572600-10587800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr1:10573400-10596000	Weak transcription	Duodenum Mucosa	Duodenum
7	chr1:10573800-10588000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr1:10573800-10588200	Weak transcription	Fetal Intestine Large	intestine
9	chr1:10575600-10588000	Weak transcription	NHLF	lung
10	chr1:10576000-10589200	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr1:10576400-10582000	Weak transcription	Thymus	Thymus
12	chr1:10576400-10582600	Weak transcription	Primary hematopoietic stem cells	blood
13	chr1:10576400-10582600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr1:10576400-10596000	Weak transcription	Dnd41	blood
15	chr1:10576800-10582200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr1:10577000-10603600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr1:10577200-10582600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr1:10577200-10584600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr1:10577400-10582000	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr1:10577400-10582000	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr1:10577400-10582200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr1:10577400-10587800	Weak transcription	Pancreas	Pancrea
23	chr1:10577400-10587800	Weak transcription	Right Atrium	heart
24	chr1:10577400-10587800	Weak transcription	HSMM	muscle
25	chr1:10577400-10588000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr1:10577400-10588000	Weak transcription	Lung	lung
27	chr1:10577400-10588000	Weak transcription	NHDF-Ad	bronchial
28	chr1:10577400-10596400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr1:10577600-10588000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr1:10577600-10588400	Weak transcription	Adipose Nuclei	Adipose
31	chr1:10577800-10582400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr1:10577800-10587800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr1:10577800-10587800	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr1:10577800-10590800	Weak transcription	Fetal Thymus	thymus
35	chr1:10578000-10582000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr1:10578000-10582400	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr1:10578000-10587800	Weak transcription	HMEC	breast
38	chr1:10578000-10588000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr1:10578200-10587800	Weak transcription	NHEK	skin
40	chr1:10578200-10588400	Weak transcription	Fetal Kidney	kidney
41	chr1:10578200-10589800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr1:10578400-10582000	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr1:10578400-10590600	Weak transcription	Placenta	Placenta
44	chr1:10578600-10581800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr1:10579200-10582200	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr1:10579200-10582400	Weak transcription	Fetal Muscle Leg	muscle
47	chr1:10579400-10582000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr1:10579400-10582600	Weak transcription	Fetal Brain Male	brain
49	chr1:10579400-10583800	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr1:10579400-10589200	Weak transcription	Gastric	stomach

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