Variant report

Variant	rs2884254
Chromosome Location	chr2:54206463-54206464
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54196999..54199592-chr2:54202573..54206522,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000068878	Chromatin interaction
ENSG00000170634	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10084355	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10186566	0.80[EUR][1000 genomes]
rs10201364	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10203576	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1058320	0.80[AMR][1000 genomes]
rs11125519	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11683654	0.85[ASN][1000 genomes]
rs11687324	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12616212	0.90[EUR][1000 genomes]
rs12713253	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13414393	0.87[ASN][1000 genomes]
rs1363062	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1363063	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1421617	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1421622	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17268179	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2111868	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2909460	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6545376	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6545378	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6545380	0.82[EUR][1000 genomes]
rs6545384	0.80[AMR][1000 genomes]
rs6715488	0.83[EUR][1000 genomes]
rs6724389	0.93[EUR][1000 genomes]
rs6749817	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs698858	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs718872	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7560947	0.80[AMR][1000 genomes]
rs7569214	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7569370	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7571086	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7591194	0.80[AMR][1000 genomes]
rs7609017	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs805308	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs805309	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs805317	0.80[AMR][1000 genomes]
rs805318	0.80[AMR][1000 genomes]
rs805320	0.81[AMR][1000 genomes]
rs805322	0.87[AMR][1000 genomes]
rs805330	0.81[AMR][1000 genomes]
rs805335	0.81[AMR][1000 genomes]
rs805341	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs805342	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs805343	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs805345	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs805358	0.82[AMR][1000 genomes]
rs805359	0.91[AMR][1000 genomes]
rs805361	0.82[AMR][1000 genomes]
rs805366	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs805367	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs805374	0.80[AMR][1000 genomes]
rs805375	0.81[AMR][1000 genomes]
rs805379	0.80[AMR][1000 genomes]
rs805380	0.81[AMR][1000 genomes]
rs805391	0.81[AMR][1000 genomes]
rs805392	0.80[AMR][1000 genomes]
rs805393	0.81[AMR][1000 genomes]
rs805402	0.83[AMR][1000 genomes]
rs805410	0.80[AMR][1000 genomes]
rs805421	0.84[AMR][1000 genomes]
rs805423	0.86[AMR][1000 genomes]
rs805424	0.88[AMR][1000 genomes]
rs805430	0.81[AMR][1000 genomes]
rs805444	0.85[AMR][1000 genomes]
rs805450	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs805453	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs809280	0.88[AMR][1000 genomes]
rs9631059	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2884254	ACYP2	cis	Esophagus Muscularis	GTEx
rs2884254	ACYP2	cis	Muscle Skeletal	GTEx

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54198600-54209000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:54198600-54212000	Weak transcription	Spleen	Spleen
3	chr2:54199000-54207200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr2:54199000-54208600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr2:54199000-54214200	Weak transcription	Stomach Mucosa	stomach
6	chr2:54199000-54214400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr2:54199000-54215600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr2:54199000-54221600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr2:54199000-54228800	Weak transcription	Aorta	Aorta
10	chr2:54199200-54207000	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr2:54199200-54207000	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr2:54199200-54207000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr2:54199200-54207000	Weak transcription	Fetal Brain Male	brain
14	chr2:54199200-54207200	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr2:54199200-54207400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr2:54199200-54207600	Weak transcription	Brain Germinal Matrix	brain
17	chr2:54199200-54207600	Weak transcription	Fetal Brain Female	brain
18	chr2:54199200-54207800	Weak transcription	Primary hematopoietic stem cells	blood
19	chr2:54199200-54208000	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr2:54199200-54209600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr2:54199200-54210600	Weak transcription	Brain Cingulate Gyrus	brain
22	chr2:54199200-54213800	Weak transcription	Psoas Muscle	Psoas
23	chr2:54199200-54213800	Weak transcription	Small Intestine	intestine
24	chr2:54199200-54214200	Weak transcription	Colonic Mucosa	Colon
25	chr2:54199200-54214200	Weak transcription	Fetal Heart	heart
26	chr2:54199200-54214200	Weak transcription	Fetal Kidney	kidney
27	chr2:54199200-54214200	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr2:54199200-54214200	Weak transcription	Rectal Smooth Muscle	rectum
29	chr2:54199200-54214200	Weak transcription	NH-A	brain
30	chr2:54199200-54214400	Weak transcription	A549	lung
31	chr2:54199200-54214600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr2:54199400-54209600	Weak transcription	HSMM	muscle
33	chr2:54200000-54214200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr2:54200200-54208200	Weak transcription	Primary B cells from cord blood	blood
35	chr2:54200200-54208400	Weak transcription	Gastric	stomach
36	chr2:54200200-54211400	Strong transcription	Fetal Muscle Leg	muscle
37	chr2:54200200-54212800	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr2:54200200-54216600	Weak transcription	Right Ventricle	heart
39	chr2:54200400-54209800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr2:54200400-54218400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr2:54200800-54208800	Strong transcription	Fetal Stomach	stomach
42	chr2:54201000-54207800	Strong transcription	Placenta	Placenta
43	chr2:54201000-54208200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr2:54201200-54208200	Strong transcription	Primary B cells from peripheral blood	blood
45	chr2:54201200-54209000	Strong transcription	Fetal Muscle Trunk	muscle
46	chr2:54201200-54209600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr2:54201400-54206600	Strong transcription	Liver	Liver
48	chr2:54201400-54208000	Strong transcription	Fetal Lung	lung
49	chr2:54201400-54208400	Strong transcription	Osteobl	bone
50	chr2:54201400-54208800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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