Variant report

Variant	rs12621225
Chromosome Location	chr2:53937177-53937178
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10171954	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10178643	0.86[ASN][1000 genomes]
rs10188142	0.85[CHB][hapmap];0.82[YRI][hapmap];0.88[ASN][1000 genomes]
rs10192626	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10201938	0.87[ASN][1000 genomes]
rs10203095	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10490471	0.82[CEU][hapmap];0.91[CHB][hapmap];0.82[ASN][1000 genomes]
rs10865275	0.83[EUR][1000 genomes]
rs11682721	0.82[EUR][1000 genomes]
rs11684084	0.81[CHB][hapmap];0.82[ASN][1000 genomes]
rs11889094	0.83[EUR][1000 genomes]
rs13414216	0.91[CHB][hapmap];0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs13432632	0.95[CHB][hapmap];0.87[JPT][hapmap];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2080715	0.82[EUR][1000 genomes]
rs2111622	0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs2111623	0.90[CHB][hapmap];0.81[JPT][hapmap];0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2160931	0.95[CHB][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2193682	0.81[CHB][hapmap];0.80[ASN][1000 genomes]
rs2193683	0.82[ASN][1000 genomes]
rs2357693	0.90[CHB][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2542574	0.80[ASN][1000 genomes]
rs2542584	0.82[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2542585	0.85[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs2542588	0.81[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs2542593	0.84[ASN][1000 genomes]
rs2692515	0.82[ASN][1000 genomes]
rs2692518	0.83[ASN][1000 genomes]
rs2692531	0.89[CEU][hapmap];0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs2692532	0.85[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2692536	0.81[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs2909263	0.84[ASN][1000 genomes]
rs2949811	0.84[ASN][1000 genomes]
rs2949812	0.83[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs3821081	0.95[CHB][hapmap];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4413193	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4671529	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4671583	0.86[CHB][hapmap]
rs56081372	0.81[EUR][1000 genomes]
rs56173218	0.82[ASN][1000 genomes]
rs6705712	0.91[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs6708095	0.95[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6713107	0.83[CEU][hapmap];0.81[CHB][hapmap];0.85[EUR][1000 genomes]
rs6727876	0.83[EUR][1000 genomes]
rs6728355	0.83[EUR][1000 genomes]
rs6738369	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6741239	0.88[EUR][1000 genomes]
rs6757393	0.81[EUR][1000 genomes]
rs7556791	0.89[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap];0.86[EUR][1000 genomes]
rs7557799	0.90[JPT][hapmap]
rs7563054	0.81[CHB][hapmap];0.81[ASN][1000 genomes]
rs7572776	0.88[ASN][1000 genomes]
rs7573991	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7596349	0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7601692	0.90[CHB][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs805438	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs805439	0.90[CHB][hapmap]
rs918207	0.85[CHB][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916267	chr2:53747525-53955999	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv984439	chr2:53861720-53955437	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1003263	chr2:53863287-54055359	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv535720	chr2:53863287-54055359	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv1011449	chr2:53894529-53947781	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1009107	chr2:53896767-53946913	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1014949	chr2:53896767-53947781	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1011400	chr2:53899956-53947781	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv834058	chr2:53900674-54072011	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	esv1844655	chr2:53929855-53972693	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12621225	ACYP2	cis	Muscle Skeletal	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:53898000-53957400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr2:53908600-53982200	Weak transcription	Small Intestine	intestine
3	chr2:53910000-53941600	Weak transcription	Colon Smooth Muscle	Colon
4	chr2:53910000-53994000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr2:53910200-53990600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr2:53918400-53994000	Weak transcription	Fetal Heart	heart
7	chr2:53925400-53979400	Weak transcription	Psoas Muscle	Psoas
8	chr2:53927600-53937200	Weak transcription	HSMM	muscle
9	chr2:53927600-53960200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr2:53933800-53937200	Strong transcription	Brain Angular Gyrus	brain
11	chr2:53933800-53938000	Strong transcription	Skeletal Muscle Female	skeletal muscle
12	chr2:53933800-53944000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr2:53934000-53937800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr2:53934200-53938200	Strong transcription	Adipose Nuclei	Adipose
15	chr2:53934200-53938400	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
16	chr2:53934200-53942200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr2:53934400-53937200	Strong transcription	Skeletal Muscle Male	skeletal muscle
18	chr2:53934400-53937400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr2:53934800-53937200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr2:53934800-53938200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr2:53934800-53939200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr2:53935000-53937200	Strong transcription	Rectal Mucosa Donor 31	rectum
23	chr2:53935000-53937400	ZNF genes & repeats	Brain Germinal Matrix	brain
24	chr2:53935200-53937200	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr2:53935200-53937200	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
26	chr2:53935200-53937200	ZNF genes & repeats	Thymus	Thymus
27	chr2:53935200-53937400	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr2:53935200-53937400	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
29	chr2:53935200-53937400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
30	chr2:53935200-53937400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr2:53935200-53937600	ZNF genes & repeats	Fetal Brain Male	brain
32	chr2:53935200-53937800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr2:53935200-53938000	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
34	chr2:53935200-53938000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr2:53935200-53938000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
36	chr2:53935200-53938200	ZNF genes & repeats	Fetal Intestine Small	intestine
37	chr2:53935200-53938400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr2:53935200-53938600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
39	chr2:53935200-53938600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
40	chr2:53935200-53939000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
41	chr2:53935400-53937200	Strong transcription	Right Ventricle	heart
42	chr2:53935400-53937600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
43	chr2:53935400-53937800	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
44	chr2:53935400-53938200	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
45	chr2:53935400-53938200	ZNF genes & repeats	Primary B cells from cord blood	blood
46	chr2:53935400-53938400	Strong transcription	Rectal Smooth Muscle	rectum
47	chr2:53935400-53938400	ZNF genes & repeats	Dnd41	blood
48	chr2:53935400-53938800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr2:53935400-53939200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr2:53935600-53937200	ZNF genes & repeats	Fetal Kidney	kidney

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