Variant report

Variant	rs2111623
Chromosome Location	chr2:53984957-53984958
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10171954	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10178643	0.88[ASN][1000 genomes]
rs10181460	0.83[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs10188142	0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs10192626	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10201938	0.89[ASN][1000 genomes]
rs10203095	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10490471	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11684084	0.84[CEU][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12621225	0.90[CHB][hapmap];0.81[JPT][hapmap];0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs13414216	0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13432632	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2111622	0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs2160929	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs2160930	0.89[TSI][hapmap]
rs2160931	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]
rs2193682	0.80[CHB][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2193683	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2357693	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2542574	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2542576	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2542579	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2542584	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2542585	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2542588	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2542593	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2692515	0.88[ASN][1000 genomes]
rs2692518	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2692531	0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2692532	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2692536	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2692537	0.81[ASN][1000 genomes]
rs2909263	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2949811	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2949812	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3770403	0.85[EUR][1000 genomes]
rs3770405	0.84[EUR][1000 genomes]
rs3821081	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4413193	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4671529	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4671583	0.95[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs56173218	0.87[ASN][1000 genomes]
rs62139835	0.80[EUR][1000 genomes]
rs6705712	0.91[CHB][hapmap];0.89[CHD][hapmap];0.86[ASN][1000 genomes]
rs6708095	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6738369	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6743627	0.81[CEU][hapmap];0.85[CHB][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs698854	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs718872	1.00[CEU][hapmap]
rs7556791	0.81[CHB][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap]
rs7557799	0.81[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes]
rs7557898	0.81[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes]
rs7572776	0.89[ASN][1000 genomes]
rs7573991	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7584474	0.80[EUR][1000 genomes]
rs7596349	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7601692	0.93[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs805322	1.00[CEU][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes]
rs805367	1.00[CEU][hapmap]
rs805373	0.84[GIH][hapmap];0.83[MEX][hapmap]
rs805374	0.92[CEU][hapmap];0.88[GIH][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes]
rs805375	0.92[CEU][hapmap];0.90[GIH][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes]
rs805410	0.93[CEU][hapmap];0.83[GIH][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap]
rs805423	0.96[CEU][hapmap];0.81[GIH][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap]
rs805433	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs805436	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs805438	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs805439	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs805450	0.96[CEU][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap]
rs918207	0.95[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	nsv979005	chr2:53982124-53989634	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2111623	ACYP2	cis	Muscle Skeletal	GTEx
rs2111623	PSME4	cis	lymphoblastoid	seeQTL
rs2111623	PSME4	cis	cerebellum	SCAN
rs2111623	C2orf73	cis	cerebellum	SCAN
rs2111623	ACYP2	cis	multi-tissue	Pritchard

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:53910000-53994000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr2:53910200-53990600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr2:53918400-53994000	Weak transcription	Fetal Heart	heart
4	chr2:53936800-53985400	Weak transcription	Stomach Smooth Muscle	stomach
5	chr2:53937000-53994400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr2:53937200-53994200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr2:53937400-53990200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr2:53937400-53994400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr2:53938400-53992400	Weak transcription	K562	blood
10	chr2:53958200-53994400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr2:53963000-53994000	Weak transcription	A549	lung
12	chr2:53967200-53990200	Weak transcription	Gastric	stomach
13	chr2:53971200-53990200	Weak transcription	Pancreas	Pancrea
14	chr2:53973400-53994400	Weak transcription	Colonic Mucosa	Colon
15	chr2:53975600-53989200	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr2:53975600-53990200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr2:53975800-53994400	Weak transcription	Fetal Kidney	kidney
18	chr2:53976600-53988600	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr2:53977800-53989600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr2:53978200-53990200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr2:53978800-53994200	Weak transcription	Rectal Smooth Muscle	rectum
22	chr2:53979200-53990200	Weak transcription	HUVEC	blood vessel
23	chr2:53979400-53994000	Weak transcription	Osteobl	bone
24	chr2:53979600-53987200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr2:53979600-53989400	Weak transcription	NH-A	brain
26	chr2:53979800-53990200	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr2:53979800-53990200	Weak transcription	Esophagus	oesophagus
28	chr2:53979800-53994200	Weak transcription	Psoas Muscle	Psoas
29	chr2:53979800-53994200	Weak transcription	NHLF	lung
30	chr2:53980000-53990200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr2:53980600-53988600	Weak transcription	GM12878-XiMat	blood
32	chr2:53980600-53990400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr2:53981600-53990200	Weak transcription	Aorta	Aorta
34	chr2:53982000-53985800	Strong transcription	Fetal Thymus	thymus
35	chr2:53982000-53988600	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr2:53982200-53985600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr2:53982400-53990200	Weak transcription	NHEK	skin
38	chr2:53982400-53990800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr2:53982400-53991600	Weak transcription	Stomach Mucosa	stomach
40	chr2:53982400-53991800	Strong transcription	Cortex derived primary cultured neurospheres	brain
41	chr2:53982400-53994400	Weak transcription	NHDF-Ad	bronchial
42	chr2:53982800-53990200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr2:53982800-53994000	Weak transcription	HMEC	breast
44	chr2:53982800-53994200	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr2:53983000-53985400	Strong transcription	Fetal Lung	lung
46	chr2:53983000-53985800	Strong transcription	Fetal Brain Female	brain
47	chr2:53983000-53987000	Strong transcription	Fetal Muscle Leg	muscle
48	chr2:53983000-53987000	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr2:53983000-53989400	Weak transcription	HSMM	muscle
50	chr2:53983000-53994000	Weak transcription	Small Intestine	intestine

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