Variant report

Variant	rs2160931
Chromosome Location	chr2:53939548-53939549
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:53938900..53941731-chr2:54013134..54015288,2	K562	blood:
2	chr2:53931144..53933214-chr2:53937294..53940246,2	K562	blood:

Variant related genes	Relation type
ENSG00000068912	Chromatin interaction
ENSG00000115239	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10171954	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10178643	0.90[ASN][1000 genomes]
rs10188142	0.91[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs10192626	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10201938	0.90[ASN][1000 genomes]
rs10203095	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10490471	0.95[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11684084	0.81[CEU][hapmap];0.84[CHB][hapmap];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12621225	0.95[CHB][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs13414216	0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13432632	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2111622	0.91[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs2111623	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2160929	0.80[CHB][hapmap];0.81[JPT][hapmap]
rs2160930	0.91[TSI][hapmap]
rs2193682	0.85[CHB][hapmap];0.80[JPT][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2193683	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2357693	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2542574	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2542576	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2542579	0.83[EUR][1000 genomes]
rs2542584	0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2542585	0.95[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.84[ASN][1000 genomes]
rs2542588	0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2542593	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2692515	0.84[ASN][1000 genomes]
rs2692518	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2692531	0.91[CHB][hapmap];0.90[JPT][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2692532	0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2692536	1.00[ASW][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];0.83[MKK][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2909263	0.86[ASN][1000 genomes]
rs2949811	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2949812	0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs3770403	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3770405	0.87[EUR][1000 genomes]
rs3821081	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4413193	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4671529	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4671583	0.91[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs56173218	0.86[ASN][1000 genomes]
rs62139835	0.82[EUR][1000 genomes]
rs6705712	0.86[CHB][hapmap];0.92[CHD][hapmap];0.88[ASN][1000 genomes]
rs6708095	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6738369	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6743627	0.80[ASW][hapmap];0.80[CHB][hapmap];0.81[CHD][hapmap];0.83[GIH][hapmap];0.81[JPT][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.86[EUR][1000 genomes]
rs698854	0.84[EUR][1000 genomes]
rs7556791	0.81[CHD][hapmap];0.83[GIH][hapmap]
rs7557799	0.86[ASW][hapmap];0.80[CHB][hapmap];0.80[GIH][hapmap];0.90[JPT][hapmap];0.91[YRI][hapmap];0.82[EUR][1000 genomes]
rs7557898	0.86[GIH][hapmap];0.81[JPT][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs7572776	0.90[ASN][1000 genomes]
rs7573991	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7584474	0.82[EUR][1000 genomes]
rs7587217	0.80[EUR][1000 genomes]
rs7596349	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7601692	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs805373	0.87[MEX][hapmap]
rs805374	0.89[CEU][hapmap];0.81[GIH][hapmap];0.84[LWK][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap]
rs805375	0.89[CEU][hapmap];0.83[GIH][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap]
rs805410	0.96[CEU][hapmap];0.81[LWK][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap]
rs805423	1.00[CEU][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap]
rs805433	0.83[EUR][1000 genomes]
rs805436	0.82[EUR][1000 genomes]
rs805438	0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs805439	0.96[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs918207	0.90[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.88[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2160931	ACYP2	cis	Esophagus Muscularis	GTEx
rs2160931	ACYP2	cis	Muscle Skeletal	GTEx
rs2160931	C2orf73	cis	cerebellum	SCAN

Chromatin state (count:116 , 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	chr2:53927600-53960200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr2:53933800-53944000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr2:53934200-53942200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr2:53936600-53939800	Weak transcription	Osteobl	bone
12	chr2:53936600-53940000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr2:53936600-53940200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr2:53936600-53941000	Strong transcription	Fetal Stomach	stomach
15	chr2:53936600-53941400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr2:53936600-53941800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr2:53936600-53941800	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr2:53936600-53944200	Strong transcription	Primary T helper cells PMA-I stimulated	--
19	chr2:53936600-53945400	Weak transcription	Colonic Mucosa	Colon
20	chr2:53936600-53968400	Weak transcription	Pancreas	Pancrea
21	chr2:53936600-53978600	Weak transcription	Hela-S3	cervix
22	chr2:53936800-53985400	Weak transcription	Stomach Smooth Muscle	stomach
23	chr2:53937000-53940400	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr2:53937000-53943400	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr2:53937000-53944200	Strong transcription	Primary B cells from peripheral blood	blood
26	chr2:53937000-53983800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr2:53937000-53994400	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr2:53937200-53940200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr2:53937200-53941200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr2:53937200-53941200	Weak transcription	Brain Angular Gyrus	brain
31	chr2:53937200-53941200	Weak transcription	Brain Anterior Caudate	brain
32	chr2:53937200-53943200	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr2:53937200-53944000	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr2:53937200-53944800	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr2:53937200-53949400	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr2:53937200-53954000	Weak transcription	Fetal Muscle Trunk	muscle
37	chr2:53937200-53955800	Weak transcription	Brain Substantia Nigra	brain
38	chr2:53937200-53961400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr2:53937200-53964400	Weak transcription	Aorta	Aorta
40	chr2:53937200-53966800	Weak transcription	Gastric	stomach
41	chr2:53937200-53978600	Weak transcription	NH-A	brain
42	chr2:53937200-53983600	Weak transcription	Right Ventricle	heart
43	chr2:53937200-53994200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr2:53937400-53940200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr2:53937400-53941200	Weak transcription	Brain Hippocampus Middle	brain
46	chr2:53937400-53941800	Strong transcription	Primary T cells from cord blood	blood
47	chr2:53937400-53943200	Weak transcription	Ovary	ovary
48	chr2:53937400-53944000	Strong transcription	Fetal Thymus	thymus
49	chr2:53937400-53945000	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr2:53937400-53945200	Weak transcription	Brain Germinal Matrix	brain

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