Variant report

Variant	rs6711105
Chromosome Location	chr2:54244912-54244913
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 103 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs10084355	0.84[EUR][1000 genomes]
rs10084374	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10167891	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10168293	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10181999	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10183655	0.85[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.86[YRI][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10186566	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11674724	0.89[ASN][1000 genomes]
rs11676462	0.85[ASN][1000 genomes]
rs11689025	0.80[ASN][1000 genomes]
rs11694711	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11884699	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11890838	0.91[CHB][hapmap];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11893270	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11896815	0.84[ASN][1000 genomes]
rs11898855	0.93[ASN][1000 genomes]
rs12713253	0.83[EUR][1000 genomes]
rs13394278	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1363062	0.85[CEU][hapmap]
rs1363063	0.80[CEU][hapmap]
rs1421617	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs1477258	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17039547	0.84[JPT][hapmap]
rs17045452	0.91[CHB][hapmap];0.81[ASN][1000 genomes]
rs17045474	0.88[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs17045488	0.87[CHB][hapmap];0.86[ASN][1000 genomes]
rs17268179	0.83[EUR][1000 genomes]
rs1877908	0.90[JPT][hapmap]
rs2111868	0.88[CEU][hapmap]
rs2112121	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2112122	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2287643	0.84[CHB][hapmap];0.85[JPT][hapmap]
rs2357896	0.85[ASN][1000 genomes]
rs2542575	0.84[CHB][hapmap];0.95[JPT][hapmap]
rs28653587	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28851028	0.83[ASN][1000 genomes]
rs2909459	0.91[CHB][hapmap]
rs3731967	0.85[CEU][hapmap];0.95[CHB][hapmap];0.83[YRI][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4671742	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4671746	0.87[ASN][1000 genomes]
rs4671747	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55649409	0.84[ASN][1000 genomes]
rs55692047	0.87[ASN][1000 genomes]
rs56302494	0.86[ASN][1000 genomes]
rs62139336	0.81[ASN][1000 genomes]
rs6545377	0.85[ASN][1000 genomes]
rs6545380	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6545381	0.92[ASN][1000 genomes]
rs66773232	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6711217	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6713088	0.93[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap]
rs6714450	0.93[ASN][1000 genomes]
rs6715488	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6724389	0.80[CEU][hapmap]
rs6742042	0.85[EUR][1000 genomes]
rs6743455	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6746965	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6748976	0.88[ASN][1000 genomes]
rs6748997	0.85[ASN][1000 genomes]
rs6749817	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs6751105	0.85[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.80[EUR][1000 genomes]
rs698855	0.83[CHB][hapmap]
rs718872	0.85[CEU][hapmap]
rs72799298	0.88[ASN][1000 genomes]
rs72904908	0.88[ASN][1000 genomes]
rs7559380	0.82[EUR][1000 genomes]
rs7559384	0.92[ASN][1000 genomes]
rs7559947	0.81[ASN][1000 genomes]
rs7564912	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7569214	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs7569370	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs7591431	0.87[ASN][1000 genomes]
rs7597188	0.80[AMR][1000 genomes]
rs7597189	0.82[ASN][1000 genomes]
rs7609017	0.81[EUR][1000 genomes]
rs805308	0.82[CEU][hapmap]
rs805309	0.88[CEU][hapmap]
rs805310	0.92[CHB][hapmap]
rs805321	0.84[CHB][hapmap]
rs805322	0.81[CEU][hapmap]
rs805328	0.85[CHB][hapmap]
rs805341	0.81[CEU][hapmap]
rs805351	0.84[CHB][hapmap]
rs805352	0.83[CHB][hapmap]
rs805365	0.83[CHB][hapmap]
rs805367	0.82[CEU][hapmap]
rs805386	0.83[CHB][hapmap]
rs805399	0.83[CHB][hapmap]
rs805401	0.83[CHB][hapmap]
rs805404	0.83[CHB][hapmap]
rs805408	0.84[CHB][hapmap]
rs805410	0.81[CEU][hapmap]
rs805426	0.83[CHB][hapmap]
rs805438	0.81[CEU][hapmap]
rs805439	0.81[CEU][hapmap]
rs805450	0.85[CEU][hapmap]
rs9631059	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[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	nsv1001246	chr2:54195654-54434832	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
2	nsv1003205	chr2:54220049-54700843	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	esv2762639	chr2:54220049-54700855	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1011790	chr2:54220049-54714553	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv1002891	chr2:54227005-54682169	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv535722	chr2:54227005-54682169	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6711105	ACYP2	cis	Muscle Skeletal	GTEx
rs6711105	ACYP2	cis	Esophagus Muscularis	GTEx
rs6711105	PSME4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54208400-54248200	Weak transcription	Lung	lung
2	chr2:54213600-54249800	Weak transcription	Left Ventricle	heart
3	chr2:54217000-54248200	Weak transcription	Gastric	stomach
4	chr2:54229200-54245800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr2:54235400-54246400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr2:54238200-54246800	Weak transcription	Spleen	Spleen
7	chr2:54240000-54248200	Weak transcription	Psoas Muscle	Psoas
8	chr2:54240200-54248000	Weak transcription	Adipose Nuclei	Adipose
9	chr2:54240200-54257000	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr2:54240600-54248200	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr2:54241400-54245600	Weak transcription	Fetal Muscle Trunk	muscle
12	chr2:54241400-54247400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr2:54241400-54248200	Weak transcription	Thymus	Thymus
14	chr2:54241800-54247600	Weak transcription	Primary B cells from cord blood	blood
15	chr2:54242200-54247600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr2:54242200-54251800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr2:54242400-54247800	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr2:54242800-54247200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr2:54242800-54247200	Weak transcription	Fetal Intestine Small	intestine
20	chr2:54243200-54247800	Weak transcription	Placenta	Placenta
21	chr2:54243400-54247200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr2:54243400-54247200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr2:54243400-54247400	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr2:54243400-54248200	Weak transcription	Pancreas	Pancrea
25	chr2:54243400-54254200	Weak transcription	Fetal Stomach	stomach
26	chr2:54243600-54246200	Weak transcription	Brain Angular Gyrus	brain
27	chr2:54243600-54247000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr2:54243600-54247600	Weak transcription	Fetal Muscle Leg	muscle
29	chr2:54243800-54246000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr2:54243800-54247200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr2:54243800-54247200	Weak transcription	Liver	Liver
32	chr2:54243800-54247600	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr2:54243800-54247600	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr2:54243800-54247600	Weak transcription	Stomach Smooth Muscle	stomach
35	chr2:54243800-54248200	Weak transcription	Fetal Lung	lung
36	chr2:54243800-54248400	Weak transcription	Brain Substantia Nigra	brain
37	chr2:54243800-54249200	Weak transcription	HSMMtube	muscle
38	chr2:54243800-54255400	Weak transcription	HepG2	liver
39	chr2:54243800-54268000	Weak transcription	Osteobl	bone
40	chr2:54243800-54268400	Weak transcription	Brain Cingulate Gyrus	brain
41	chr2:54243800-54269800	Weak transcription	Brain Anterior Caudate	brain
42	chr2:54244000-54246200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr2:54244000-54246200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr2:54244000-54248200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr2:54244400-54246200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr2:54244400-54246400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr2:54244400-54247400	Weak transcription	NHDF-Ad	bronchial
48	chr2:54244400-54254200	Weak transcription	Ovary	ovary
49	chr2:54244800-54245200	Strong transcription	Primary T cells from cord blood	blood

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