Variant report

Variant	rs6545380
Chromosome Location	chr2:54240578-54240579
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:54190729..54192357-chr2:54239475..54241800,2	MCF-7	breast:
2	chr2:54238943..54240796-chr2:54245575..54247733,2	K562	blood:
3	chr2:54195961..54197468-chr2:54240342..54242610,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ACYP2-6	chr2:54234735-54240630	NONHSAT070717

Extended variants
information (count: 67 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10084355	0.81[EUR][1000 genomes]
rs10084374	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10167891	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10168293	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10181999	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10183655	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10186566	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10201364	0.81[EUR][1000 genomes]
rs11674724	0.92[ASN][1000 genomes]
rs11689025	0.83[ASN][1000 genomes]
rs11694711	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11884699	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11890838	0.83[ASN][1000 genomes]
rs11893270	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11898855	0.86[ASN][1000 genomes]
rs13394278	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1421617	0.80[EUR][1000 genomes]
rs1477258	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17045452	0.83[ASN][1000 genomes]
rs17045474	0.83[ASN][1000 genomes]
rs2112121	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2112122	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28653587	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2884254	0.82[EUR][1000 genomes]
rs28851028	0.86[ASN][1000 genomes]
rs2909459	0.81[ASN][1000 genomes]
rs3731967	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4671742	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4671746	0.90[ASN][1000 genomes]
rs4671747	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55692047	0.90[ASN][1000 genomes]
rs56302494	0.89[ASN][1000 genomes]
rs62139336	0.83[ASN][1000 genomes]
rs6545376	0.81[EUR][1000 genomes]
rs6545377	0.87[ASN][1000 genomes]
rs6545378	0.82[EUR][1000 genomes]
rs6545381	0.85[ASN][1000 genomes]
rs66773232	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6711105	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6711217	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6714450	0.86[ASN][1000 genomes]
rs6715488	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6742042	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6743455	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6746965	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6748976	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6748997	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6749817	0.81[EUR][1000 genomes]
rs72799298	0.91[ASN][1000 genomes]
rs72904908	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7559384	0.85[ASN][1000 genomes]
rs7559947	0.83[ASN][1000 genomes]
rs7564912	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7569214	0.83[EUR][1000 genomes]
rs7569370	0.83[EUR][1000 genomes]
rs7591431	0.90[ASN][1000 genomes]
rs7597188	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7597189	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs805310	0.81[ASN][1000 genomes]
rs805344	0.81[ASN][1000 genomes]
rs9631059	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[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
rs6545380	ACYP2	cis	Muscle Skeletal	GTEx
rs6545380	ACYP2	cis	Esophagus Muscularis	GTEx
rs6545380	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	chr2:54211400-54243000	Weak transcription	Fetal Muscle Leg	muscle
3	chr2:54213600-54249800	Weak transcription	Left Ventricle	heart
4	chr2:54215000-54242800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:54216400-54242000	Weak transcription	Fetal Intestine Small	intestine
6	chr2:54217000-54248200	Weak transcription	Gastric	stomach
7	chr2:54226600-54243000	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr2:54228800-54243400	Weak transcription	Fetal Lung	lung
9	chr2:54229000-54243000	Weak transcription	Right Atrium	heart
10	chr2:54229200-54245800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr2:54234400-54242800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr2:54235400-54242800	Weak transcription	Ovary	ovary
13	chr2:54235400-54246400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr2:54235800-54243600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr2:54237200-54243000	Weak transcription	Brain Hippocampus Middle	brain
16	chr2:54237200-54243000	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr2:54237400-54243000	Weak transcription	Brain Cingulate Gyrus	brain
18	chr2:54238000-54242400	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr2:54238200-54246800	Weak transcription	Spleen	Spleen
20	chr2:54238400-54242600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr2:54238600-54242600	Weak transcription	NHDF-Ad	bronchial
22	chr2:54239200-54242800	Enhancers	Primary T cells fromperipheralblood	blood
23	chr2:54239600-54240600	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr2:54239600-54241000	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr2:54239600-54241000	Enhancers	Primary T killer memory cells from peripheral blood	blood
26	chr2:54239600-54241200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
27	chr2:54239600-54241200	Enhancers	Colon Smooth Muscle	Colon
28	chr2:54239600-54241600	Enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr2:54239600-54242000	Enhancers	Primary B cells from peripheral blood	blood
30	chr2:54239600-54242800	Enhancers	Primary T helper cells fromperipheralblood	blood
31	chr2:54239800-54241800	Enhancers	Fetal Thymus	thymus
32	chr2:54239800-54242200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr2:54239800-54242800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
34	chr2:54240000-54241000	Weak transcription	Primary hematopoietic stem cells	blood
35	chr2:54240000-54241000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr2:54240000-54241200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
37	chr2:54240000-54241800	Enhancers	Primary B cells from cord blood	blood
38	chr2:54240000-54242400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr2:54240000-54242600	Weak transcription	Brain Substantia Nigra	brain
40	chr2:54240000-54242800	Weak transcription	Placenta	Placenta
41	chr2:54240000-54248200	Weak transcription	Psoas Muscle	Psoas
42	chr2:54240200-54241000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
43	chr2:54240200-54242400	Weak transcription	Stomach Smooth Muscle	stomach
44	chr2:54240200-54242800	Weak transcription	Brain Anterior Caudate	brain
45	chr2:54240200-54243000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr2:54240200-54243000	Weak transcription	Rectal Smooth Muscle	rectum
47	chr2:54240200-54243800	Enhancers	Primary T cells from cord blood	blood
48	chr2:54240200-54248000	Weak transcription	Adipose Nuclei	Adipose
49	chr2:54240200-54257000	Weak transcription	Skeletal Muscle Female	skeletal muscle

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