Variant report

Variant	rs7556791
Chromosome Location	chr2:53906935-53906936
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10171954	0.80[ASN][1000 genomes]
rs10188142	0.81[CHD][hapmap]
rs10490471	0.81[CHB][hapmap]
rs10865275	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11125515	0.95[ASN][1000 genomes]
rs11682721	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11684084	0.90[CHB][hapmap];0.91[ASN][1000 genomes]
rs11889094	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11902691	0.94[ASN][1000 genomes]
rs12611475	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12620583	0.93[ASN][1000 genomes]
rs12621225	0.89[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap];0.86[EUR][1000 genomes]
rs13414216	0.81[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs13428898	0.82[EUR][1000 genomes]
rs2080715	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2111623	0.81[CHB][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap]
rs2160929	0.95[CHB][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs2160930	0.88[GIH][hapmap]
rs2160931	0.81[CHD][hapmap];0.83[GIH][hapmap]
rs2193682	0.90[CHB][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs2193683	0.91[ASN][1000 genomes]
rs2357693	0.81[CHB][hapmap];0.86[GIH][hapmap];0.80[ASN][1000 genomes]
rs2542584	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs2542585	0.81[CHB][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap]
rs2542588	0.81[CHB][hapmap];0.81[CHD][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap]
rs2692531	0.81[CEU][hapmap]
rs2692532	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs2692536	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs2949812	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs3770403	0.88[ASN][1000 genomes]
rs3770405	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs3821081	0.86[GIH][hapmap]
rs4671529	0.82[ASN][1000 genomes]
rs56081372	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56291505	0.97[ASN][1000 genomes]
rs62139772	0.91[ASN][1000 genomes]
rs62139780	0.97[ASN][1000 genomes]
rs62139783	0.94[ASN][1000 genomes]
rs62139835	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6705712	0.81[CHB][hapmap];0.82[ASN][1000 genomes]
rs6713107	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6714891	0.97[ASN][1000 genomes]
rs6727876	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6728355	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6741239	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6743627	0.95[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.95[ASN][1000 genomes]
rs6757393	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7557799	0.95[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.97[ASN][1000 genomes]
rs7557898	0.90[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.97[ASN][1000 genomes]
rs7563054	0.90[CHB][hapmap];0.89[CHD][hapmap];0.84[JPT][hapmap];0.92[ASN][1000 genomes]
rs7573991	0.81[ASN][1000 genomes]
rs7584474	0.97[ASN][1000 genomes]
rs7587217	0.96[ASN][1000 genomes]
rs7601692	0.81[CHB][hapmap];0.81[CHD][hapmap];0.86[GIH][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs805438	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs805439	0.81[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7556791	ACYP2	cis	Muscle Skeletal	GTEx
rs7556791	C2orf73	cis	cerebellum	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:53874200-53935000	Weak transcription	Pancreas	Pancrea
2	chr2:53881400-53934400	Weak transcription	Stomach Smooth Muscle	stomach
3	chr2:53885600-53925000	Weak transcription	Fetal Intestine Small	intestine
4	chr2:53885800-53911800	Weak transcription	Adipose Nuclei	Adipose
5	chr2:53888200-53934200	Weak transcription	Lung	lung
6	chr2:53888400-53935200	Weak transcription	Fetal Brain Male	brain
7	chr2:53888600-53935200	Weak transcription	Hela-S3	cervix
8	chr2:53889000-53935800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr2:53892600-53918800	Weak transcription	Left Ventricle	heart
10	chr2:53893400-53915200	Weak transcription	Ovary	ovary
11	chr2:53893800-53926800	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr2:53894200-53920800	Weak transcription	Duodenum Mucosa	Duodenum
13	chr2:53894400-53912200	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr2:53894400-53914400	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr2:53894400-53925000	Weak transcription	Fetal Muscle Trunk	muscle
16	chr2:53894400-53933800	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr2:53894600-53911200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr2:53895000-53911800	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr2:53895400-53919000	Weak transcription	Fetal Intestine Large	intestine
20	chr2:53895400-53921200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr2:53895400-53925800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr2:53895400-53926200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr2:53895600-53914800	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr2:53895600-53921400	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr2:53895800-53916800	Weak transcription	Brain Anterior Caudate	brain
26	chr2:53895800-53926200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr2:53896000-53913000	Weak transcription	Fetal Muscle Leg	muscle
28	chr2:53896000-53918800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr2:53896200-53911200	Weak transcription	Liver	Liver
30	chr2:53896200-53918400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr2:53896400-53926000	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr2:53896800-53910200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr2:53896800-53910800	Weak transcription	Primary B cells from peripheral blood	blood
34	chr2:53896800-53918800	Weak transcription	Fetal Brain Female	brain
35	chr2:53896800-53924800	Weak transcription	Thymus	Thymus
36	chr2:53896800-53936600	Weak transcription	Aorta	Aorta
37	chr2:53897000-53910400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr2:53897000-53911400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr2:53897400-53910200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr2:53897400-53910200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr2:53897400-53912000	Weak transcription	Primary hematopoietic stem cells	blood
42	chr2:53897600-53911600	Weak transcription	Dnd41	blood
43	chr2:53897800-53910800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr2:53897800-53911000	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr2:53897800-53911600	Weak transcription	Fetal Thymus	thymus
46	chr2:53898000-53910200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr2:53898000-53910200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr2:53898000-53914800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr2:53898000-53918800	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr2:53898000-53957400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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