Variant report

Variant	rs2000052
Chromosome Location	chr3:194997620-194997621
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 93 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10439949	0.87[CEU][hapmap]
rs10933704	0.80[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11709417	0.90[EUR][1000 genomes]
rs11715185	0.98[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11715202	0.81[EUR][1000 genomes]
rs11718226	0.87[CEU][hapmap]
rs12054139	0.87[CEU][hapmap]
rs12629884	0.81[AMR][1000 genomes]
rs13317782	0.81[AMR][1000 genomes]
rs13320698	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1832666	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1890853	0.91[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.81[JPT][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1994880	0.87[CEU][hapmap]
rs2000051	0.95[CEU][hapmap];0.93[LWK][hapmap];0.85[MKK][hapmap];0.82[TSI][hapmap];0.91[YRI][hapmap];0.98[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs2029708	0.91[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs2050806	0.91[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2131685	0.81[AMR][1000 genomes]
rs2275518	0.87[CEU][hapmap]
rs2275519	0.91[CEU][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes]
rs2410792	0.81[AMR][1000 genomes]
rs2410804	0.81[EUR][1000 genomes]
rs4461369	0.89[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs4677666	0.80[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4677669	0.87[CEU][hapmap]
rs4677828	0.91[CEU][hapmap];0.84[GIH][hapmap];0.81[MEX][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4677839	0.91[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4677840	0.91[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4677843	0.86[CEU][hapmap]
rs4677844	0.91[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes]
rs57124286	0.93[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs58067895	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59563484	0.87[EUR][1000 genomes]
rs62285259	0.94[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs62287061	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62287066	0.86[EUR][1000 genomes]
rs6437373	0.87[CEU][hapmap]
rs6437375	0.86[CEU][hapmap]
rs6437376	0.91[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6437471	0.87[CEU][hapmap]
rs6763335	0.87[CEU][hapmap]
rs6763588	0.91[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6771771	0.87[CEU][hapmap]
rs6781311	0.81[AMR][1000 genomes]
rs6785382	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6791563	0.87[CEU][hapmap]
rs6800221	0.87[CEU][hapmap]
rs6800562	0.91[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes]
rs6801007	0.87[CEU][hapmap]
rs6801315	0.86[CEU][hapmap]
rs6801750	0.91[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6803763	0.87[CEU][hapmap]
rs716898	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7611090	0.87[CEU][hapmap]
rs7617936	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7621133	0.87[CEU][hapmap]
rs7622180	0.95[CEU][hapmap];0.82[TSI][hapmap];0.90[EUR][1000 genomes]
rs7623135	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7627671	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7632534	0.91[EUR][1000 genomes]
rs7635603	0.91[CEU][hapmap];0.92[CHB][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes]
rs9288744	0.91[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap];0.85[MEX][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9288746	0.91[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap]
rs9681021	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9812506	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9813425	0.82[EUR][1000 genomes]
rs9814214	0.91[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.81[JPT][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9840309	1.00[CHB][hapmap]
rs9844354	0.91[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9847544	0.91[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9855453	0.87[CEU][hapmap]
rs9859279	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9859822	1.00[CHB][hapmap];0.82[CHD][hapmap]
rs9859902	0.87[CEU][hapmap]
rs9860798	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9864603	0.91[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9866537	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9868768	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9879305	0.87[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007697	chr3:194554814-195009930	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	nsv536873	chr3:194554814-195009930	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
3	nsv1009796	chr3:194737333-195124248	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
4	nsv1014826	chr3:194834615-195631793	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
5	nsv536876	chr3:194834615-195631793	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
6	nsv533904	chr3:194868329-195438728	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	65 gene(s)	inside rSNPs	diseases
7	nsv1010168	chr3:194874494-195135790	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
8	nsv536877	chr3:194874494-195135790	Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
9	nsv997956	chr3:194879534-195087539	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS 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
10	nsv536878	chr3:194879534-195087539	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer 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
11	esv1832781	chr3:194902818-195528226	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases
12	nsv432508	chr3:194916131-195478861	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	59 gene(s)	inside rSNPs	diseases
13	nsv432510	chr3:194935314-195478861	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	59 gene(s)	inside rSNPs	diseases
14	nsv1005519	chr3:194964301-195340515	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
15	nsv432511	chr3:194986167-195479748	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2000052	XXYLT1	cis	Skin Sun Exposed Lower leg	GTEx
rs2000052	XXYLT1	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:194992400-195009000	Weak transcription	Spleen	Spleen
2	chr3:194992600-195003600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:194992600-195003600	Weak transcription	Small Intestine	intestine
4	chr3:194992600-195008200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:194992600-195008800	Weak transcription	Lung	lung
6	chr3:194992600-195090000	Weak transcription	Aorta	Aorta
7	chr3:194992800-195003600	Weak transcription	Esophagus	oesophagus
8	chr3:194992800-195003600	Weak transcription	Fetal Muscle Trunk	muscle
9	chr3:194992800-195003600	Weak transcription	Fetal Muscle Leg	muscle
10	chr3:194992800-195003600	Weak transcription	Left Ventricle	heart
11	chr3:194992800-195003600	Weak transcription	Psoas Muscle	Psoas
12	chr3:194992800-195003600	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr3:194992800-195004800	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr3:194992800-195005400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr3:194992800-195008600	Weak transcription	Ovary	ovary
16	chr3:194992800-195039800	Weak transcription	Fetal Brain Male	brain
17	chr3:194992800-195039800	Weak transcription	Right Ventricle	heart
18	chr3:194993000-194997800	Weak transcription	Fetal Intestine Large	intestine
19	chr3:194993000-194997800	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr3:194993000-194998000	Weak transcription	Fetal Lung	lung
21	chr3:194993000-194998400	Weak transcription	Thymus	Thymus
22	chr3:194993000-194998600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr3:194993000-194998800	Weak transcription	Duodenum Mucosa	Duodenum
24	chr3:194993000-194999200	Weak transcription	Primary B cells from peripheral blood	blood
25	chr3:194993000-194999200	Weak transcription	Placenta	Placenta
26	chr3:194993000-194999400	Weak transcription	Primary T cells from cord blood	blood
27	chr3:194993000-194999400	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr3:194993000-194999400	Weak transcription	Rectal Smooth Muscle	rectum
29	chr3:194993000-195001200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr3:194993000-195003000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr3:194993000-195003400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr3:194993000-195003400	Weak transcription	Adipose Nuclei	Adipose
33	chr3:194993000-195003600	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr3:194993000-195003600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr3:194993000-195003600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr3:194993000-195003600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr3:194993000-195003600	Weak transcription	Fetal Intestine Small	intestine
38	chr3:194993000-195003600	Weak transcription	Fetal Stomach	stomach
39	chr3:194993000-195003600	Weak transcription	Gastric	stomach
40	chr3:194993000-195003600	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr3:194993000-195003600	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr3:194993000-195003600	Weak transcription	Stomach Mucosa	stomach
43	chr3:194993000-195003800	Weak transcription	Fetal Brain Female	brain
44	chr3:194993000-195003800	Weak transcription	Stomach Smooth Muscle	stomach
45	chr3:194993000-195004000	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr3:194993000-195004800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr3:194993000-195005000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr3:194993000-195005200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr3:194993000-195005600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr3:194993000-195005600	Weak transcription	HSMM	muscle

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