Variant report

Variant	rs3803973
Chromosome Location	chr20:13497355-13497356
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs1012242	0.84[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1474954	0.85[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1474955	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1474956	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.92[ASN][1000 genomes]
rs1474957	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1884796	0.83[EUR][1000 genomes]
rs1884797	0.83[EUR][1000 genomes]
rs1963182	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1998123	0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs2001178	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2057256	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2057257	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2070306	0.85[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.92[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2273477	0.81[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2327790	0.85[EUR][1000 genomes]
rs2327791	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2876357	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34590652	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3761889	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3761890	0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.80[TSI][hapmap];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3827702	0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3827703	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4813130	0.83[EUR][1000 genomes]
rs4813132	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4813134	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4813135	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4814233	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.92[ASN][1000 genomes]
rs4814234	0.81[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4814235	0.82[EUR][1000 genomes]
rs4814239	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4814246	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs527865	0.81[EUR][1000 genomes]
rs6033705	0.85[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6033722	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6033724	0.83[EUR][1000 genomes]
rs6033749	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.96[ASN][1000 genomes]
rs6033756	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6042135	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs6042141	0.81[CEU][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs6042162	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6042188	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6042192	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6042195	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6042211	0.81[CEU][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs6042218	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6074604	0.84[ASN][1000 genomes]
rs6074605	0.81[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6074610	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.92[ASN][1000 genomes]
rs6074616	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6079035	0.95[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap]
rs6079042	0.95[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs6079043	0.84[ASN][1000 genomes]
rs6079048	0.90[ASN][1000 genomes]
rs6079049	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6079062	0.87[ASN][1000 genomes]
rs6079063	0.95[CHB][hapmap];0.86[JPT][hapmap];0.80[YRI][hapmap];0.87[ASN][1000 genomes]
rs6079086	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6079097	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6079102	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6079115	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs6105087	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6105118	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6105119	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6109854	1.00[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6109858	0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6109861	0.80[ASN][1000 genomes]
rs6109862	0.95[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.90[ASN][1000 genomes]
rs6109918	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6109923	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6109935	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6109946	0.83[EUR][1000 genomes]
rs6131471	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.90[ASN][1000 genomes]
rs6134862	0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6134870	1.00[CHB][hapmap];0.86[JPT][hapmap];0.81[YRI][hapmap];0.87[ASN][1000 genomes]
rs6134895	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6514411	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7265499	0.81[EUR][1000 genomes]
rs743183	0.81[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs911014	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs932568	0.81[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1061303	chr20:13395546-13810990	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv585435	chr20:13410638-13582476	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv916202	chr20:13421724-14043615	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv1059817	chr20:13422602-13807968	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv458871	chr20:13447896-13573415	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv585436	chr20:13447896-13573415	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv1066810	chr20:13451869-14432454	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13463800-13505400	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr20:13470200-13505800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr20:13473400-13505800	Weak transcription	HSMM	muscle
4	chr20:13478200-13503800	Weak transcription	Gastric	stomach
5	chr20:13483200-13509200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr20:13484000-13499000	Weak transcription	Aorta	Aorta
7	chr20:13484000-13502600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr20:13484000-13502600	Weak transcription	Primary T cells from cord blood	blood
9	chr20:13484000-13502600	Weak transcription	Fetal Stomach	stomach
10	chr20:13485000-13502600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr20:13485000-13543600	Weak transcription	Small Intestine	intestine
12	chr20:13485800-13497400	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr20:13486200-13502600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr20:13487600-13515000	Weak transcription	Brain Germinal Matrix	brain
15	chr20:13488200-13502600	Weak transcription	Lung	lung
16	chr20:13488200-13502600	Weak transcription	Ovary	ovary
17	chr20:13489000-13502600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr20:13489000-13502600	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr20:13489000-13502600	Weak transcription	Fetal Intestine Large	intestine
20	chr20:13489200-13514600	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr20:13489600-13497600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr20:13489600-13499000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr20:13490400-13502800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr20:13490400-13509600	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr20:13490800-13502800	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr20:13491800-13503400	Weak transcription	Liver	Liver
27	chr20:13492200-13499600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr20:13492200-13503800	Weak transcription	Right Ventricle	heart
29	chr20:13492200-13505600	Weak transcription	Spleen	Spleen
30	chr20:13492200-13567000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr20:13492600-13502600	Weak transcription	Brain Hippocampus Middle	brain
32	chr20:13493600-13502800	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr20:13493600-13505400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr20:13493600-13507600	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr20:13493600-13510800	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr20:13493600-13519200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr20:13493800-13497600	Strong transcription	Primary B cells from cord blood	blood
38	chr20:13493800-13504000	Weak transcription	Fetal Muscle Trunk	muscle
39	chr20:13494000-13502600	Weak transcription	Duodenum Mucosa	Duodenum
40	chr20:13494000-13502600	Weak transcription	A549	lung
41	chr20:13494000-13504000	Weak transcription	Fetal Intestine Small	intestine
42	chr20:13494000-13505400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr20:13494000-13507800	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr20:13494000-13512400	Weak transcription	Placenta	Placenta
45	chr20:13494000-13515600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr20:13494200-13502800	Weak transcription	Fetal Muscle Leg	muscle
47	chr20:13494200-13516000	Weak transcription	Colonic Mucosa	Colon
48	chr20:13494400-13502600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr20:13494400-13506400	Weak transcription	Primary hematopoietic stem cells	blood
50	chr20:13494400-13507600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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