Variant report

Variant	rs6042212
Chromosome Location	chr20:13529922-13529923
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 149 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:141)

rs_ID	r²[population]
rs1024208	1.00[JPT][hapmap]
rs1028849	1.00[JPT][hapmap]
rs11698396	0.86[ASN][1000 genomes]
rs12329562	0.83[ASN][1000 genomes]
rs12329620	1.00[CEU][hapmap]
rs12479480	1.00[JPT][hapmap]
rs12479520	1.00[JPT][hapmap]
rs12479594	1.00[JPT][hapmap]
rs12479849	1.00[JPT][hapmap]
rs12480266	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs12480276	1.00[JPT][hapmap]
rs12480277	1.00[JPT][hapmap]
rs12480457	1.00[JPT][hapmap]
rs12480587	1.00[JPT][hapmap]
rs13041649	0.86[ASN][1000 genomes]
rs1812562	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs2038437	0.82[CEU][hapmap]
rs2073323	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2145140	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs2327755	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs2327789	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28444692	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2876356	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3789343	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3789344	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3789345	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3789350	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4411781	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6033694	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs6033695	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs6033699	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs6033702	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs6033703	0.82[CEU][hapmap]
rs6033704	0.82[CEU][hapmap]
rs6033708	0.82[CEU][hapmap]
rs6033712	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs6033718	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs6033720	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6033723	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6033727	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6033731	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6033733	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6033735	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6033736	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6033737	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6033741	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6033745	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6033755	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6033782	1.00[JPT][hapmap]
rs6042069	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs6042077	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs6042081	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs6042083	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs6042084	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs6042089	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs6042093	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs6042108	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs6042111	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs6042113	1.00[JPT][hapmap]
rs6042130	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs6042136	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs6042142	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs6042154	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs6042156	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6042167	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6042174	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6042176	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6042179	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6042181	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6042183	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6042184	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6042186	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6042242	1.00[JPT][hapmap]
rs6105082	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs6105083	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs6105088	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs6105089	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs6105092	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs6105093	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs6105094	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs6105097	1.00[CEU][hapmap]
rs6105108	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs6105109	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs6105115	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6105116	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6109863	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs6109866	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs6109869	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs6109870	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs6109871	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs6109872	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs6109873	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs6109883	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs6109885	1.00[CEU][hapmap]
rs6109886	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs6109888	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs6109889	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs6109895	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs6109896	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs6109901	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs6109904	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs6109906	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6109908	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6109913	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6109915	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6109972	1.00[JPT][hapmap]
rs6109985	1.00[JPT][hapmap]
rs6131478	0.84[ASN][1000 genomes]
rs6131480	0.84[ASN][1000 genomes]
rs6131481	0.84[ASN][1000 genomes]
rs6131482	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6134882	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6134883	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6134885	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6134890	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6134892	0.82[ASN][1000 genomes]
rs6134893	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6134894	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6134896	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6134897	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6134899	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6134904	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6134907	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6134908	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6134909	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6134911	0.86[ASN][1000 genomes]
rs6134913	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6134914	0.86[ASN][1000 genomes]
rs6134915	0.86[ASN][1000 genomes]
rs7274078	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs73080067	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73080080	0.90[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs73086022	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73086039	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8115098	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8123095	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8124555	0.80[EUR][1000 genomes]
rs8126063	0.82[ASN][1000 genomes]
rs8184309	0.86[ASN][1000 genomes]
rs927122	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs9653627	1.00[CEU][hapmap];1.00[JPT][hapmap]

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:60 , 50 per page) page: 1 2

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	chr20:13497800-13563400	Weak transcription	Pancreas	Pancrea
4	chr20:13503000-13537600	Weak transcription	Psoas Muscle	Psoas
5	chr20:13503000-13538200	Weak transcription	Ovary	ovary
6	chr20:13506400-13558800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr20:13508000-13534000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr20:13508000-13542000	Weak transcription	Fetal Intestine Small	intestine
9	chr20:13508000-13563600	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr20:13508200-13556400	Weak transcription	Fetal Muscle Trunk	muscle
11	chr20:13508400-13538000	Weak transcription	HepG2	liver
12	chr20:13508400-13546600	Weak transcription	Fetal Kidney	kidney
13	chr20:13508400-13550400	Weak transcription	GM12878-XiMat	blood
14	chr20:13508400-13556000	Weak transcription	HSMM	muscle
15	chr20:13508400-13559600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr20:13508400-13563400	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr20:13509200-13536200	Weak transcription	Fetal Intestine Large	intestine
18	chr20:13509200-13548200	Weak transcription	Duodenum Mucosa	Duodenum
19	chr20:13509200-13556000	Weak transcription	Fetal Stomach	stomach
20	chr20:13509800-13536200	Weak transcription	Fetal Muscle Leg	muscle
21	chr20:13509800-13538600	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr20:13509800-13547400	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr20:13512800-13548400	Weak transcription	Left Ventricle	heart
24	chr20:13512800-13556000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr20:13513800-13547600	Weak transcription	Primary hematopoietic stem cells	blood
26	chr20:13514000-13532000	Weak transcription	Primary B cells from cord blood	blood
27	chr20:13514000-13536200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr20:13514800-13536600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr20:13514800-13541000	Weak transcription	Primary B cells from peripheral blood	blood
30	chr20:13514800-13546400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr20:13515000-13605600	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr20:13516600-13538200	Weak transcription	Thymus	Thymus
33	chr20:13526800-13561800	Weak transcription	Stomach Mucosa	stomach
34	chr20:13526800-13613800	Weak transcription	Hela-S3	cervix
35	chr20:13527000-13530400	Genic enhancers	Dnd41	blood
36	chr20:13527000-13556000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr20:13527200-13534800	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr20:13527200-13540000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr20:13527400-13532000	Weak transcription	Fetal Lung	lung
40	chr20:13527400-13535400	Weak transcription	NHEK	skin
41	chr20:13527400-13535400	Weak transcription	Osteobl	bone
42	chr20:13527400-13536800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr20:13527400-13539000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr20:13527400-13552200	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr20:13527400-13560000	Weak transcription	HSMMtube	muscle
46	chr20:13527400-13562200	Weak transcription	Aorta	Aorta
47	chr20:13527400-13563400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr20:13527600-13532800	Weak transcription	A549	lung
49	chr20:13527600-13535200	Weak transcription	NH-A	brain
50	chr20:13527600-13538200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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