Variant report

Variant	rs6724389
Chromosome Location	chr2:54212835-54212836
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54196132..54198667-chr2:54212629..54214327,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000068878	Chromatin interaction
ENSG00000170634	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10084355	0.90[EUR][1000 genomes]
rs10201364	0.93[EUR][1000 genomes]
rs10203576	0.81[EUR][1000 genomes]
rs10208233	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1058320	0.85[CEU][hapmap]
rs1075265	0.86[CEU][hapmap]
rs1118618	0.83[AMR][1000 genomes]
rs11687324	0.82[EUR][1000 genomes]
rs12616212	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12713253	0.90[EUR][1000 genomes]
rs1363062	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs1363063	0.86[CEU][hapmap];0.81[EUR][1000 genomes]
rs1363065	1.00[ASN][1000 genomes]
rs1421617	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs1421622	0.81[EUR][1000 genomes]
rs17268179	0.90[EUR][1000 genomes]
rs2111868	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs2287642	0.86[CEU][hapmap]
rs2884254	0.93[EUR][1000 genomes]
rs2909460	0.88[EUR][1000 genomes]
rs6545376	0.93[EUR][1000 genomes]
rs6545378	0.93[EUR][1000 genomes]
rs6545379	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6545389	1.00[CHB][hapmap]
rs6749817	0.88[CEU][hapmap];0.91[EUR][1000 genomes]
rs718872	0.93[CEU][hapmap];0.81[EUR][1000 genomes]
rs7569214	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs7569370	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs7571086	0.85[EUR][1000 genomes]
rs7609017	0.82[EUR][1000 genomes]
rs805308	0.90[CEU][hapmap];0.89[EUR][1000 genomes]
rs805309	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs805322	0.82[CEU][hapmap]
rs805341	0.89[CEU][hapmap]
rs805343	0.80[EUR][1000 genomes]
rs805345	0.87[EUR][1000 genomes]
rs805367	0.86[CEU][hapmap]
rs805438	0.82[CEU][hapmap]
rs805439	0.82[CEU][hapmap]
rs805450	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs805453	0.82[EUR][1000 genomes]
rs918357	0.85[CEU][hapmap]
rs929734	0.86[CEU][hapmap]

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
rs6724389	ACYP2	cis	Muscle Skeletal	GTEx
rs6724389	ACYP2	cis	Esophagus Muscularis	GTEx

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54199000-54214200	Weak transcription	Stomach Mucosa	stomach
2	chr2:54199000-54214400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr2:54199000-54215600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr2:54199000-54221600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr2:54199000-54228800	Weak transcription	Aorta	Aorta
6	chr2:54199200-54213800	Weak transcription	Psoas Muscle	Psoas
7	chr2:54199200-54213800	Weak transcription	Small Intestine	intestine
8	chr2:54199200-54214200	Weak transcription	Colonic Mucosa	Colon
9	chr2:54199200-54214200	Weak transcription	Fetal Heart	heart
10	chr2:54199200-54214200	Weak transcription	Fetal Kidney	kidney
11	chr2:54199200-54214200	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr2:54199200-54214200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr2:54199200-54214200	Weak transcription	NH-A	brain
14	chr2:54199200-54214400	Weak transcription	A549	lung
15	chr2:54199200-54214600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr2:54200000-54214200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr2:54200200-54216600	Weak transcription	Right Ventricle	heart
18	chr2:54200400-54218400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr2:54202600-54214200	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr2:54202600-54214400	Weak transcription	NHDF-Ad	bronchial
21	chr2:54202800-54214800	Weak transcription	NHLF	lung
22	chr2:54202800-54215800	Weak transcription	NHEK	skin
23	chr2:54203200-54214200	Weak transcription	Colon Smooth Muscle	Colon
24	chr2:54203600-54214800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr2:54203800-54214200	Weak transcription	Brain Anterior Caudate	brain
26	chr2:54204400-54226400	Weak transcription	Pancreas	Pancrea
27	chr2:54204600-54214000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr2:54204600-54214200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr2:54205000-54213800	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr2:54205200-54222600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr2:54206000-54214200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr2:54206000-54214200	Weak transcription	GM12878-XiMat	blood
33	chr2:54206000-54216600	Weak transcription	Esophagus	oesophagus
34	chr2:54206000-54221600	Weak transcription	Thymus	Thymus
35	chr2:54206000-54226400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr2:54206200-54214200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr2:54206200-54214200	Weak transcription	Adipose Nuclei	Adipose
38	chr2:54206200-54214200	Weak transcription	Brain Hippocampus Middle	brain
39	chr2:54206200-54214200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr2:54206200-54214200	Weak transcription	Brain Substantia Nigra	brain
41	chr2:54206200-54214400	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr2:54206400-54220000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr2:54207800-54213000	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr2:54208200-54214000	Weak transcription	Liver	Liver
45	chr2:54208200-54214200	Weak transcription	HSMMtube	muscle
46	chr2:54208200-54221400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr2:54208400-54214000	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr2:54208400-54214000	Weak transcription	Osteobl	bone
49	chr2:54208400-54214200	Weak transcription	Fetal Lung	lung
50	chr2:54208400-54248200	Weak transcription	Lung	lung

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