Variant report

Variant	rs17268179
Chromosome Location	chr2:54264013-54264014
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54263866..54266283-chr2:54268179..54270997,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ACYP2-4	chr2:54263335-54264887	NONHSAT070722

Extended variants
information (count: 75 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10084355	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10084374	0.81[EUR][1000 genomes]
rs10181999	0.83[EUR][1000 genomes]
rs10201364	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10203576	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10208233	0.84[EUR][1000 genomes]
rs1058320	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1075265	0.93[CEU][hapmap]
rs11125519	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11683654	0.94[CHB][hapmap];0.83[JPT][hapmap];0.94[ASN][1000 genomes]
rs11687324	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11893270	0.83[EUR][1000 genomes]
rs12616212	0.94[EUR][1000 genomes]
rs12713253	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13414393	0.86[CHB][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs1363062	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1363063	0.93[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1421617	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1421622	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1833498	0.81[AMR][1000 genomes]
rs2111868	0.92[CEU][hapmap];0.92[CHB][hapmap];0.84[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2112122	0.81[EUR][1000 genomes]
rs2287642	0.93[CEU][hapmap]
rs2884254	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2909460	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs41385746	0.86[JPT][hapmap]
rs4671872	0.86[CEU][hapmap]
rs6545376	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6545378	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6545384	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6545388	0.86[CEU][hapmap]
rs6711105	0.83[EUR][1000 genomes]
rs6711217	0.81[EUR][1000 genomes]
rs6713088	0.80[CEU][hapmap]
rs6724389	0.93[CEU][hapmap];0.90[EUR][1000 genomes]
rs6743455	0.83[EUR][1000 genomes]
rs6749817	0.96[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs698858	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs718872	0.93[CEU][hapmap];0.94[CHB][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7560947	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7566894	0.86[CEU][hapmap]
rs7569214	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7569370	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7571086	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7591194	0.83[AMR][1000 genomes]
rs7609017	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs805308	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs805309	1.00[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs805322	0.89[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap]
rs805341	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs805343	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs805345	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs805359	0.82[AMR][1000 genomes]
rs805360	0.87[CHB][hapmap]
rs805366	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs805367	0.89[CEU][hapmap];0.94[CHB][hapmap];0.84[AMR][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]
rs805410	0.82[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap]
rs805412	0.94[CHB][hapmap]
rs805423	0.85[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap]
rs805450	0.92[CEU][hapmap];0.87[CHB][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs805453	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs918357	0.92[CEU][hapmap]
rs929734	0.93[CEU][hapmap]
rs959286	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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
7	nsv1011690	chr2:54255361-54700843	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
8	nsv431069	chr2:54260132-54434049	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17268179	ACYP2	cis	Muscle Skeletal	GTEx
rs17268179	ACYP2	cis	Esophagus Muscularis	GTEx

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54243800-54268000	Weak transcription	Osteobl	bone
2	chr2:54243800-54268400	Weak transcription	Brain Cingulate Gyrus	brain
3	chr2:54243800-54269800	Weak transcription	Brain Anterior Caudate	brain
4	chr2:54246800-54275200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr2:54248600-54278000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr2:54248600-54289800	Weak transcription	Fetal Lung	lung
7	chr2:54248800-54275600	Weak transcription	Primary B cells from cord blood	blood
8	chr2:54254600-54267400	Weak transcription	Brain Substantia Nigra	brain
9	chr2:54254600-54269800	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr2:54254800-54269600	Weak transcription	Colon Smooth Muscle	Colon
11	chr2:54258000-54272200	Weak transcription	Primary hematopoietic stem cells	blood
12	chr2:54258200-54264400	Weak transcription	Fetal Brain Female	brain
13	chr2:54258200-54266200	Weak transcription	Fetal Intestine Small	intestine
14	chr2:54258200-54266400	Weak transcription	Psoas Muscle	Psoas
15	chr2:54258200-54267000	Weak transcription	Ovary	ovary
16	chr2:54258200-54269600	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr2:54258200-54269800	Weak transcription	Fetal Heart	heart
18	chr2:54258200-54269800	Weak transcription	Fetal Muscle Leg	muscle
19	chr2:54258200-54270000	Weak transcription	HepG2	liver
20	chr2:54259000-54267200	Weak transcription	Adipose Nuclei	Adipose
21	chr2:54260000-54269800	Weak transcription	Stomach Smooth Muscle	stomach
22	chr2:54260000-54272200	Weak transcription	Primary B cells from peripheral blood	blood
23	chr2:54260400-54278200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr2:54261200-54269600	Weak transcription	Brain Hippocampus Middle	brain
25	chr2:54262000-54268200	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr2:54263800-54264200	Strong transcription	Primary T cells from cord blood	blood

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