Variant report

Variant	rs10490471
Chromosome Location	chr2:53996583-53996584
allele	C/G
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	MAFK	chr2:53996482-53996746	HepG2	liver:	n/a	chr2:53996649-53996669
2	RCOR1	chr2:53996217-53997095	K562	blood:	n/a	n/a
3	IRF1	chr2:53995920-53996745	K562	blood:	n/a	chr2:53996450-53996462 chr2:53996120-53996134 chr2:53996036-53996050
4	CEBPB	chr2:53996413-53997530	K562	blood:	n/a	chr2:53996593-53996610 chr2:53997344-53997355
5	POLR2A	chr2:53994401-53997166	GM18505	blood:	n/a	n/a
6	CEBPB	chr2:53996466-53997533	K562	blood:	n/a	chr2:53996593-53996610 chr2:53997344-53997355
7	BACH1	chr2:53996489-53996756	K562	blood:	n/a	n/a
8	MYC	chr2:53996322-53997560	K562	blood:	n/a	n/a
9	MAFF	chr2:53996510-53996696	HepG2	liver:	n/a	n/a
10	POLR2A	chr2:53996573-53996815	Hela-S3	cervix:	n/a	n/a
11	MAFK	chr2:53996240-53996853	K562	blood:	n/a	chr2:53996649-53996669
12	POLR2A	chr2:53993983-53998651	GM12878	blood:	n/a	n/a
13	MAFF	chr2:53996473-53996802	K562	blood:	n/a	n/a
14	POLR2A	chr2:53994075-53999332	K562	blood:	n/a	n/a
15	EP300	chr2:53996232-53997835	K562	blood:	n/a	chr2:53997335-53997342 chr2:53997481-53997488 chr2:53997557-53997566 chr2:53997461-53997470
16	POLR2A	chr2:53996150-53998649	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr2:53996538-53996728	GM12891	blood:	n/a	n/a
18	MAFK	chr2:53996530-53996791	HepG2	liver:	n/a	chr2:53996649-53996669

No.	Distal block	Cell Line	Cell type
1	chr2:53996518..54000180-chr2:54012874..54016675,4	K562	blood:
2	chr2:53993518..53997677-chr2:54010995..54015634,7	MCF-7	breast:
3	chr2:53993579..53997009-chr2:54011416..54015067,4	MCF-7	breast:

Variant related genes	Relation type
GPR75-ASB3	TF binding region
ENSG00000115239	Chromatin interaction
ENSG00000068912	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10171954	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10178643	0.86[ASN][1000 genomes]
rs10181460	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10188142	0.95[CHB][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs10192626	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10201938	0.86[ASN][1000 genomes]
rs10203095	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11684084	0.81[CHB][hapmap];0.81[ASN][1000 genomes]
rs12621225	0.82[CEU][hapmap];0.91[CHB][hapmap];0.82[ASN][1000 genomes]
rs13414216	0.91[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs13417926	0.81[ASN][1000 genomes]
rs13432632	0.95[CHB][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2111622	0.95[CHB][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs2111623	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2160929	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs2160931	0.95[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2193682	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs2193683	0.81[ASN][1000 genomes]
rs2357693	1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2542574	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2542576	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2542579	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2542584	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]
rs2542585	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2542588	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2542593	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2692515	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2692518	0.93[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2692531	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2692532	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2692536	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2692537	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2909263	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2949811	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2949812	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3821081	1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4413193	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4671529	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4671583	0.95[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs56173218	0.84[ASN][1000 genomes]
rs6705712	0.91[CHB][hapmap];0.84[ASN][1000 genomes]
rs6708095	0.95[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs6713107	0.81[CHB][hapmap]
rs6738369	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6743627	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs698854	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7556791	0.81[CHB][hapmap]
rs7557799	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs7557898	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs7572776	0.88[ASN][1000 genomes]
rs7573991	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7596349	0.80[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs7601692	0.90[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs805433	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs805436	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs805438	1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs805439	1.00[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs918207	0.95[CHB][hapmap];0.90[JPT][hapmap];0.88[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10490471	ACYP2	cis	Muscle Skeletal	GTEx

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:53994200-53996600	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr2:53995400-54003600	Weak transcription	Small Intestine	intestine
3	chr2:53995600-53996600	Weak transcription	Gastric	stomach
4	chr2:53995600-53996800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr2:53995600-54005800	Weak transcription	HSMM	muscle
6	chr2:53995600-54007400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr2:53995600-54007400	Weak transcription	Fetal Muscle Leg	muscle
8	chr2:53995600-54007800	Weak transcription	Placenta	Placenta
9	chr2:53995600-54008400	Weak transcription	Ovary	ovary
10	chr2:53995600-54009000	Weak transcription	Fetal Muscle Trunk	muscle
11	chr2:53995600-54009000	Weak transcription	Lung	lung
12	chr2:53995600-54011400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr2:53995600-54011400	Weak transcription	Right Atrium	heart
14	chr2:53995600-54011600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr2:53995600-54012000	Weak transcription	Left Ventricle	heart
16	chr2:53995600-54012800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:53995800-53996600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr2:53995800-53996600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr2:53995800-53996800	Flanking Active TSS	Dnd41	blood
20	chr2:53995800-53997000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr2:53995800-53999600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr2:53995800-54000600	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr2:53995800-54000600	Weak transcription	Fetal Intestine Small	intestine
24	chr2:53995800-54001000	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr2:53995800-54001200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr2:53995800-54003000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr2:53995800-54006800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr2:53995800-54008600	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr2:53995800-54011400	Weak transcription	Colon Smooth Muscle	Colon
30	chr2:53995800-54011600	Weak transcription	Psoas Muscle	Psoas
31	chr2:53995800-54011800	Weak transcription	Right Ventricle	heart
32	chr2:53995800-54012000	Weak transcription	Adipose Nuclei	Adipose
33	chr2:53995800-54012200	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr2:53995800-54012400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr2:53995800-54012600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr2:53996000-53996600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
37	chr2:53996000-53996600	Weak transcription	Brain Anterior Caudate	brain
38	chr2:53996000-53996600	Flanking Active TSS	Hela-S3	cervix
39	chr2:53996000-53996800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
40	chr2:53996000-53996800	Weak transcription	Stomach Smooth Muscle	stomach
41	chr2:53996000-53996800	Flanking Active TSS	GM12878-XiMat	blood
42	chr2:53996000-53998400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr2:53996000-54000800	Weak transcription	Fetal Intestine Large	intestine
44	chr2:53996000-54001200	Weak transcription	Primary hematopoietic stem cells	blood
45	chr2:53996000-54004400	Weak transcription	Osteobl	bone
46	chr2:53996000-54005800	Weak transcription	Liver	Liver
47	chr2:53996000-54006800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr2:53996000-54009000	Weak transcription	Brain Substantia Nigra	brain
49	chr2:53996000-54011000	Weak transcription	Fetal Brain Male	brain
50	chr2:53996000-54011200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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