Variant report

Variant	rs2357693
Chromosome Location	chr2:53962836-53962837
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 77 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10171954	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10178643	0.95[ASN][1000 genomes]
rs10188142	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs10192626	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10201938	0.96[ASN][1000 genomes]
rs10203095	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10490471	1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11684084	0.84[CEU][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12621225	0.90[CHB][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs13414216	0.90[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13432632	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2009142	0.83[LWK][hapmap]
rs2111622	0.95[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs2111623	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]
rs2160929	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs2160930	0.89[TSI][hapmap]
rs2160931	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]
rs2193682	0.80[CHB][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2193683	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2542574	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2542576	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2542579	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2542584	1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2542585	0.87[ASW][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2542588	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2542593	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2692515	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2692518	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2692531	0.95[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2692532	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2692536	1.00[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2692537	0.83[ASN][1000 genomes]
rs2909263	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2949811	0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2949812	1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3770403	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3770405	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3821081	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4413193	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4671529	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4671583	0.95[CHB][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap];0.88[ASN][1000 genomes]
rs56173218	0.94[ASN][1000 genomes]
rs62139835	0.83[ASN][1000 genomes]
rs6705712	0.91[CHB][hapmap];0.97[CHD][hapmap];0.82[JPT][hapmap];0.93[ASN][1000 genomes]
rs6708095	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6713107	0.80[ASN][1000 genomes]
rs6738369	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6741239	0.80[ASN][1000 genomes]
rs6743627	0.81[CEU][hapmap];0.85[CHB][hapmap];0.87[CHD][hapmap];0.86[GIH][hapmap];0.81[JPT][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6747749	0.84[LWK][hapmap]
rs698854	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7556791	0.81[CHB][hapmap];0.86[GIH][hapmap];0.80[ASN][1000 genomes]
rs7557799	0.81[CEU][hapmap];0.85[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs7557898	0.81[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];0.83[GIH][hapmap];0.81[JPT][hapmap];0.93[TSI][hapmap];0.83[ASN][1000 genomes]
rs7563054	0.82[CHD][hapmap];0.80[ASN][1000 genomes]
rs7572776	0.96[ASN][1000 genomes]
rs7573991	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7584474	0.83[ASN][1000 genomes]
rs7587217	0.82[ASN][1000 genomes]
rs7596349	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7601692	0.93[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs805322	1.00[CEU][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes]
rs805359	0.80[EUR][1000 genomes]
rs805373	0.81[GIH][hapmap];0.88[MEX][hapmap]
rs805374	0.92[CEU][hapmap];0.83[GIH][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes]
rs805375	0.92[CEU][hapmap];0.85[GIH][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes]
rs805410	0.93[CEU][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap]
rs805423	0.96[CEU][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap]
rs805433	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs805436	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs805438	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs805439	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.89[LWK][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs918207	0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.80[LWK][hapmap];0.82[YRI][hapmap];0.98[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	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
rs2357693	PSME4	cis	lymphoblastoid	seeQTL
rs2357693	C2orf73	cis	cerebellum	SCAN
rs2357693	ACYP2	cis	Muscle Skeletal	GTEx

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:53908600-53982200	Weak transcription	Small Intestine	intestine
2	chr2:53910000-53994000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr2:53910200-53990600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr2:53918400-53994000	Weak transcription	Fetal Heart	heart
5	chr2:53925400-53979400	Weak transcription	Psoas Muscle	Psoas
6	chr2:53936600-53968400	Weak transcription	Pancreas	Pancrea
7	chr2:53936600-53978600	Weak transcription	Hela-S3	cervix
8	chr2:53936800-53985400	Weak transcription	Stomach Smooth Muscle	stomach
9	chr2:53937000-53983800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr2:53937000-53994400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr2:53937200-53964400	Weak transcription	Aorta	Aorta
12	chr2:53937200-53966800	Weak transcription	Gastric	stomach
13	chr2:53937200-53978600	Weak transcription	NH-A	brain
14	chr2:53937200-53983600	Weak transcription	Right Ventricle	heart
15	chr2:53937200-53994200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr2:53937400-53964000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr2:53937400-53979600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr2:53937400-53990200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr2:53937400-53994400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr2:53938000-53974800	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr2:53938000-53974800	Weak transcription	Placenta	Placenta
22	chr2:53938200-53967000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr2:53938200-53975200	Weak transcription	Duodenum Mucosa	Duodenum
24	chr2:53938400-53963600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr2:53938400-53969400	Weak transcription	Rectal Smooth Muscle	rectum
26	chr2:53938400-53969600	Weak transcription	Esophagus	oesophagus
27	chr2:53938400-53975000	Weak transcription	Fetal Kidney	kidney
28	chr2:53938400-53982800	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr2:53938400-53983400	Weak transcription	HSMMtube	muscle
30	chr2:53938400-53992400	Weak transcription	K562	blood
31	chr2:53938600-53972000	Weak transcription	HSMM	muscle
32	chr2:53941800-53974400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr2:53941800-53976400	Weak transcription	Colon Smooth Muscle	Colon
34	chr2:53943800-53974800	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr2:53943800-53983600	Weak transcription	Ovary	ovary
36	chr2:53943800-53983600	Weak transcription	Thymus	Thymus
37	chr2:53943800-53983800	Weak transcription	Left Ventricle	heart
38	chr2:53944000-53974600	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr2:53945800-53968400	Weak transcription	Brain Anterior Caudate	brain
40	chr2:53949800-53974200	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr2:53952200-53978600	Weak transcription	Osteobl	bone
42	chr2:53952400-53983600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr2:53952600-53974800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr2:53954000-53963000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr2:53954400-53972000	Weak transcription	NHDF-Ad	bronchial
46	chr2:53954800-53969600	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr2:53954800-53982000	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr2:53954800-53983800	Weak transcription	Lung	lung
49	chr2:53955400-53965800	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr2:53955800-53974600	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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