Variant report

Variant	rs2542584
Chromosome Location	chr2:54009844-54009845
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SRF	chr2:54009639-54009962	H1-hESC	embryonic stem cell:	n/a	chr2:54009804-54009813 chr2:54009797-54009814 chr2:54009804-54009815 chr2:54009802-54009815 chr2:54009800-54009817 chr2:54009803-54009814 chr2:54009801-54009816 chr2:54009799-54009817 chr2:54009802-54009815

No.	Distal block	Cell Line	Cell type
1	chr2:54006024..54008035-chr2:54009628..54012351,2	K562	blood:
2	chr2:54008638..54010431-chr2:54015192..54016791,2	K562	blood:
3	chr2:54008226..54010680-chr2:54013442..54015348,3	MCF-7	breast:

Variant related genes	Relation type
ERLEC1	TF binding region
ENSG00000115239	Chromatin interaction
ENSG00000068912	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10171954	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10178643	0.86[ASN][1000 genomes]
rs10181460	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10188142	0.95[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs10192626	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10201938	0.87[ASN][1000 genomes]
rs10203095	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10490471	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11684084	0.81[CHB][hapmap];0.80[JPT][hapmap];0.82[ASN][1000 genomes]
rs12621225	0.82[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs13414216	0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs13417926	0.82[ASN][1000 genomes]
rs13432632	0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2111622	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs2111623	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2160929	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs2160931	0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2193682	0.81[CHB][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs2193683	0.82[ASN][1000 genomes]
rs2357693	1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2542574	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2542576	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2542579	0.87[ASN][1000 genomes]
rs2542585	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2542588	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2542593	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2692515	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2692518	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2692531	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2692532	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2692536	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2692537	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2909263	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2949811	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2949812	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3821081	1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4413193	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4671529	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4671583	0.95[CHB][hapmap];0.91[JPT][hapmap];0.97[YRI][hapmap];0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs56173218	0.85[ASN][1000 genomes]
rs6705712	0.91[CHB][hapmap];0.84[ASN][1000 genomes]
rs6708095	0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6713107	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs6738369	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6743627	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs698854	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7556791	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs7557799	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs7557898	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs7572776	0.88[ASN][1000 genomes]
rs7573991	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7596349	0.80[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7601692	0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs805433	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs805436	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs805438	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs805439	1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs918207	0.95[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv1009829	chr2:53980562-54051927	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2542584	ACYP2	cis	Muscle Skeletal	GTEx
rs2542584	ACYP2	cis	Esophagus Muscularis	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:53995600-54011400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:53995600-54011400	Weak transcription	Right Atrium	heart
3	chr2:53995600-54011600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:53995600-54012000	Weak transcription	Left Ventricle	heart
5	chr2:53995600-54012800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:53995800-54011400	Weak transcription	Colon Smooth Muscle	Colon
7	chr2:53995800-54011600	Weak transcription	Psoas Muscle	Psoas
8	chr2:53995800-54011800	Weak transcription	Right Ventricle	heart
9	chr2:53995800-54012000	Weak transcription	Adipose Nuclei	Adipose
10	chr2:53995800-54012200	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr2:53995800-54012400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr2:53995800-54012600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr2:53996000-54011000	Weak transcription	Fetal Brain Male	brain
14	chr2:53996000-54011200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr2:53996000-54011600	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr2:53996000-54011600	Weak transcription	Fetal Lung	lung
17	chr2:53996000-54011800	Weak transcription	NHDF-Ad	bronchial
18	chr2:53996200-54011000	Weak transcription	Brain Angular Gyrus	brain
19	chr2:53996200-54011400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr2:53996200-54012600	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr2:53996400-54011000	Weak transcription	NHEK	skin
22	chr2:53996400-54011200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr2:53996400-54011200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr2:53996400-54011200	Weak transcription	Brain Cingulate Gyrus	brain
25	chr2:53996400-54011400	Weak transcription	Thymus	Thymus
26	chr2:53996400-54011600	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr2:53996400-54011800	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr2:53996400-54011800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr2:53996400-54012200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr2:53996400-54012400	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr2:53996600-54010600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr2:53996600-54011400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr2:53996800-54010800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr2:53996800-54011200	Weak transcription	Duodenum Mucosa	Duodenum
35	chr2:53997000-54010800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr2:53997000-54011400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr2:53997000-54011600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr2:53997200-54010600	Weak transcription	Hela-S3	cervix
39	chr2:53998200-54010600	Weak transcription	HepG2	liver
40	chr2:53998800-54011200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr2:54002200-54010400	Strong transcription	Fetal Thymus	thymus
42	chr2:54002800-54011200	Weak transcription	HMEC	breast
43	chr2:54002800-54011400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr2:54003400-54011400	Weak transcription	Fetal Heart	heart
45	chr2:54003800-54010000	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr2:54004000-54012600	Weak transcription	Small Intestine	intestine
47	chr2:54004200-54010200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr2:54004200-54012200	Weak transcription	Rectal Smooth Muscle	rectum
49	chr2:54004600-54010800	Weak transcription	GM12878-XiMat	blood
50	chr2:54004600-54011200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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