Variant report

Variant	rs6109935
Chromosome Location	chr20:13519837-13519838
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 90 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs1012242	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1474954	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1474955	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1474956	0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs1474957	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1884796	0.81[CEU][hapmap];0.90[EUR][1000 genomes]
rs1884797	0.81[CEU][hapmap];0.90[EUR][1000 genomes]
rs1963182	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1998123	0.84[CEU][hapmap];0.91[EUR][1000 genomes]
rs2001178	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2057256	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2057257	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2057258	0.86[YRI][hapmap]
rs2070306	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2273477	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2327790	0.94[EUR][1000 genomes]
rs2327791	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2876357	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34590652	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3761889	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3761890	0.90[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3803973	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]
rs3827702	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3827703	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4813130	0.90[EUR][1000 genomes]
rs4813132	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4813134	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4813135	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4814233	0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs4814234	0.90[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.84[YRI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4814235	0.88[EUR][1000 genomes]
rs4814239	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4814246	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs593846	0.80[EUR][1000 genomes]
rs6033705	0.95[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.87[YRI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6033722	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6033724	0.90[EUR][1000 genomes]
rs6033749	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6033756	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6042135	0.86[CEU][hapmap];0.90[EUR][1000 genomes]
rs6042141	0.90[CEU][hapmap];0.91[EUR][1000 genomes]
rs6042162	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6042188	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6042192	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6042195	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6042211	0.90[CEU][hapmap];0.91[EUR][1000 genomes]
rs6042218	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6042224	0.81[JPT][hapmap]
rs6074604	0.80[ASN][1000 genomes]
rs6074605	0.81[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6074610	1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs6074616	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6079035	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs6079042	0.95[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs6079043	0.80[ASN][1000 genomes]
rs6079048	0.85[ASN][1000 genomes]
rs6079049	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6079062	0.82[ASN][1000 genomes]
rs6079063	0.95[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs6079086	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6079097	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6079102	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6079115	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6105087	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6105118	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6105119	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6109854	0.85[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6109858	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6109861	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6109862	0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs6109918	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6109923	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6109946	0.90[EUR][1000 genomes]
rs6131471	0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs6134862	0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs6134870	1.00[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs6134895	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6514411	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs743183	0.90[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs910969	0.80[EUR][1000 genomes]
rs911014	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs932568	0.90[CEU][hapmap];1.00[CHB][hapmap];0.80[JPT][hapmap];0.83[YRI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
8	nsv912687	chr20:13507057-13591596	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13485000-13543600	Weak transcription	Small Intestine	intestine
2	chr20:13492200-13567000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr20:13496000-13520200	Weak transcription	HSMMtube	muscle
4	chr20:13497800-13563400	Weak transcription	Pancreas	Pancrea
5	chr20:13503000-13537600	Weak transcription	Psoas Muscle	Psoas
6	chr20:13503000-13538200	Weak transcription	Ovary	ovary
7	chr20:13504200-13527000	Strong transcription	Dnd41	blood
8	chr20:13506400-13558800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr20:13507800-13526200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr20:13508000-13527000	Weak transcription	NHEK	skin
11	chr20:13508000-13534000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr20:13508000-13542000	Weak transcription	Fetal Intestine Small	intestine
13	chr20:13508000-13563600	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr20:13508200-13525000	Weak transcription	A549	lung
15	chr20:13508200-13556400	Weak transcription	Fetal Muscle Trunk	muscle
16	chr20:13508400-13538000	Weak transcription	HepG2	liver
17	chr20:13508400-13546600	Weak transcription	Fetal Kidney	kidney
18	chr20:13508400-13550400	Weak transcription	GM12878-XiMat	blood
19	chr20:13508400-13556000	Weak transcription	HSMM	muscle
20	chr20:13508400-13559600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr20:13508400-13563400	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr20:13509000-13527200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr20:13509000-13528000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr20:13509200-13520600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr20:13509200-13536200	Weak transcription	Fetal Intestine Large	intestine
26	chr20:13509200-13548200	Weak transcription	Duodenum Mucosa	Duodenum
27	chr20:13509200-13556000	Weak transcription	Fetal Stomach	stomach
28	chr20:13509600-13527200	Weak transcription	Liver	Liver
29	chr20:13509800-13526600	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr20:13509800-13536200	Weak transcription	Fetal Muscle Leg	muscle
31	chr20:13509800-13538600	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr20:13509800-13547400	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr20:13512800-13548400	Weak transcription	Left Ventricle	heart
34	chr20:13512800-13556000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr20:13513000-13526800	Weak transcription	Aorta	Aorta
36	chr20:13513800-13547600	Weak transcription	Primary hematopoietic stem cells	blood
37	chr20:13514000-13532000	Weak transcription	Primary B cells from cord blood	blood
38	chr20:13514000-13536200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr20:13514400-13526200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr20:13514400-13527000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr20:13514800-13536600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr20:13514800-13541000	Weak transcription	Primary B cells from peripheral blood	blood
43	chr20:13514800-13546400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr20:13515000-13605600	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr20:13516400-13529000	Weak transcription	Fetal Thymus	thymus
46	chr20:13516600-13528600	Weak transcription	Primary T cells from cord blood	blood
47	chr20:13516600-13538200	Weak transcription	Thymus	Thymus

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