Variant report

Variant	rs6545376
Chromosome Location	chr2:54214822-54214823
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:54214773..54216416-chr2:54226494..54228805,2	MCF-7	breast:
2	chr2:54214676..54216240-chr2:54269746..54271307,2	MCF-7	breast:
3	chr2:54213667..54216386-chr2:54218063..54220465,2	K562	blood:

Extended variants
information (count: 68 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10084355	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10201364	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10203576	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1058320	0.92[CEU][hapmap]
rs1075265	0.93[CEU][hapmap]
rs11125519	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11683654	0.94[CHB][hapmap];0.85[ASN][1000 genomes]
rs11687324	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12616212	0.89[EUR][1000 genomes]
rs12713253	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13414393	0.86[CHB][hapmap];0.87[ASN][1000 genomes]
rs1363062	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1363063	0.93[CEU][hapmap];0.94[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1421617	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1421622	0.83[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	0.92[CEU][hapmap];0.92[CHB][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2287642	0.93[CEU][hapmap]
rs2884254	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2909460	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4671872	0.86[CEU][hapmap]
rs6545378	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6545380	0.81[EUR][1000 genomes]
rs6545384	0.80[AMR][1000 genomes]
rs6545388	0.86[CEU][hapmap]
rs6713088	0.80[CEU][hapmap]
rs6715488	0.83[EUR][1000 genomes]
rs6724389	0.93[CEU][hapmap];0.93[EUR][1000 genomes]
rs6749817	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs698858	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs718872	0.93[CEU][hapmap];0.94[CHB][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7566894	0.86[CEU][hapmap]
rs7569214	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7569370	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7571086	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7609017	0.86[EUR][1000 genomes]
rs805308	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs805309	1.00[CEU][hapmap];0.93[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs805322	0.89[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap];0.85[AMR][1000 genomes]
rs805341	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs805342	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs805343	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs805345	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs805358	0.80[AMR][1000 genomes]
rs805359	0.87[AMR][1000 genomes]
rs805360	0.87[CHB][hapmap]
rs805361	0.80[AMR][1000 genomes]
rs805366	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs805367	0.89[CEU][hapmap];0.94[CHB][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs805373	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs805374	0.81[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap]
rs805375	0.81[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap]
rs805402	0.81[AMR][1000 genomes]
rs805410	0.82[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes]
rs805412	0.94[CHB][hapmap]
rs805421	0.84[AMR][1000 genomes]
rs805423	0.85[CEU][hapmap];0.93[CHB][hapmap];0.87[JPT][hapmap];0.82[AMR][1000 genomes]
rs805424	0.80[AMR][1000 genomes]
rs805438	0.89[CEU][hapmap]
rs805439	0.89[CEU][hapmap]
rs805444	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs805450	0.92[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs805453	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs809280	0.80[AMR][1000 genomes]
rs918357	0.92[CEU][hapmap]
rs929734	0.93[CEU][hapmap]
rs9631059	0.81[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
rs6545376	ACYP2	cis	Muscle Skeletal	GTEx
rs6545376	ACYP2	cis	Esophagus Muscularis	GTEx

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54199000-54215600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr2:54199000-54221600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr2:54199000-54228800	Weak transcription	Aorta	Aorta
4	chr2:54200200-54216600	Weak transcription	Right Ventricle	heart
5	chr2:54200400-54218400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr2:54202800-54215800	Weak transcription	NHEK	skin
7	chr2:54204400-54226400	Weak transcription	Pancreas	Pancrea
8	chr2:54205200-54222600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr2:54206000-54216600	Weak transcription	Esophagus	oesophagus
10	chr2:54206000-54221600	Weak transcription	Thymus	Thymus
11	chr2:54206000-54226400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr2:54206400-54220000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr2:54208200-54221400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr2:54208400-54248200	Weak transcription	Lung	lung
15	chr2:54208600-54216600	Weak transcription	Gastric	stomach
16	chr2:54208600-54219000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr2:54208600-54220200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr2:54208800-54216600	Weak transcription	Brain Angular Gyrus	brain
19	chr2:54209000-54221400	Weak transcription	Fetal Thymus	thymus
20	chr2:54209000-54221600	Weak transcription	Dnd41	blood
21	chr2:54211200-54216600	Weak transcription	Stomach Smooth Muscle	stomach
22	chr2:54211200-54219000	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr2:54211200-54220600	Weak transcription	Primary hematopoietic stem cells	blood
24	chr2:54211400-54217800	Weak transcription	Fetal Muscle Trunk	muscle
25	chr2:54211400-54220200	Weak transcription	Primary B cells from cord blood	blood
26	chr2:54211400-54243000	Weak transcription	Fetal Muscle Leg	muscle
27	chr2:54211600-54215800	Weak transcription	Ovary	ovary
28	chr2:54211800-54215800	Weak transcription	Fetal Intestine Small	intestine
29	chr2:54212400-54215000	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr2:54212600-54215400	Enhancers	HepG2	liver
31	chr2:54213600-54216200	Weak transcription	Right Atrium	heart
32	chr2:54213600-54249800	Weak transcription	Left Ventricle	heart
33	chr2:54213800-54215000	Enhancers	Primary T helper cells PMA-I stimulated	--
34	chr2:54213800-54217200	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr2:54214000-54215000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
36	chr2:54214000-54215000	Enhancers	Brain Inferior Temporal Lobe	brain
37	chr2:54214000-54215000	Enhancers	Duodenum Mucosa	Duodenum
38	chr2:54214000-54215000	Enhancers	Duodenum Smooth Muscle	Duodenum
39	chr2:54214000-54215000	Enhancers	Rectal Mucosa Donor 31	rectum
40	chr2:54214000-54215200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr2:54214000-54215200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr2:54214000-54215200	Enhancers	Liver	Liver
43	chr2:54214000-54215400	Enhancers	Osteobl	bone
44	chr2:54214200-54215000	Enhancers	Adipose Nuclei	Adipose
45	chr2:54214200-54215000	Enhancers	Brain Anterior Caudate	brain
46	chr2:54214200-54215000	Enhancers	Brain Hippocampus Middle	brain
47	chr2:54214200-54215000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
48	chr2:54214200-54215000	Enhancers	Brain Substantia Nigra	brain
49	chr2:54214200-54215000	Enhancers	Colon Smooth Muscle	Colon
50	chr2:54214200-54215000	Enhancers	Fetal Brain Female	brain

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