Variant report

Variant	rs6042211
Chromosome Location	chr20:13527257-13527258
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:13439318..13440167-chr20:13526983..13527752,3	MCF-7	breast:
2	chr20:13100265..13100795-chr20:13526790..13527749,2	MCF-7	breast:
3	chr20:13526812..13528359-chr20:13536217..13539188,2	K562	blood:
4	chr20:13305433..13306398-chr20:13526637..13527817,4	MCF-7	breast:
5	chr20:13439332..13440129-chr20:13526875..13527507,2	K562	blood:
6	chr20:13439454..13440147-chr20:13526949..13528062,4	MCF-7	breast:
7	chr20:13099205..13100228-chr20:13526624..13527393,3	MCF-7	breast:
8	chr20:13305737..13306312-chr20:13526618..13527354,2	K562	blood:
9	chr20:13404058..13404784-chr20:13526885..13527481,2	MCF-7	breast:

No data

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1012242	0.94[CEU][hapmap];0.91[EUR][1000 genomes]
rs1474954	0.95[CEU][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs1474955	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs1474957	0.87[EUR][1000 genomes]
rs1884796	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1884797	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1963182	0.85[EUR][1000 genomes]
rs1998123	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.90[TSI][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2001178	0.95[CEU][hapmap];0.94[EUR][1000 genomes]
rs2057256	0.90[CEU][hapmap];0.93[EUR][1000 genomes]
rs2057257	0.89[EUR][1000 genomes]
rs2070306	0.92[TSI][hapmap];0.88[EUR][1000 genomes]
rs2273477	0.90[CEU][hapmap];0.90[TSI][hapmap];0.89[EUR][1000 genomes]
rs2327790	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2327791	0.88[EUR][1000 genomes]
rs2876357	0.89[EUR][1000 genomes]
rs3761890	0.85[TSI][hapmap]
rs3803973	0.81[CEU][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs3827702	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs3827703	0.90[CEU][hapmap];0.89[EUR][1000 genomes]
rs4813130	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4813132	0.88[CEU][hapmap]
rs4813134	0.81[CEU][hapmap];0.89[EUR][1000 genomes]
rs4813135	0.90[CEU][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes]
rs4814234	0.90[CEU][hapmap];0.85[EUR][1000 genomes]
rs4814235	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4814239	0.89[EUR][1000 genomes]
rs4814246	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs6033705	0.84[CEU][hapmap];0.85[EUR][1000 genomes]
rs6033722	0.91[EUR][1000 genomes]
rs6033724	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6033749	0.86[TSI][hapmap]
rs6033756	0.90[CEU][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs6042135	0.90[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6042141	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6042162	0.90[EUR][1000 genomes]
rs6042188	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs6042192	0.90[CEU][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs6042218	0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs6074605	0.81[CEU][hapmap];0.80[TSI][hapmap];0.80[EUR][1000 genomes]
rs6074616	0.88[EUR][1000 genomes]
rs6079049	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs6079086	0.87[EUR][1000 genomes]
rs6079097	0.95[CEU][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes]
rs6079102	0.84[EUR][1000 genomes]
rs6079115	0.90[CEU][hapmap];0.85[EUR][1000 genomes]
rs6105087	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs6105118	0.90[EUR][1000 genomes]
rs6105119	0.90[EUR][1000 genomes]
rs6109854	0.85[CEU][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs6109858	0.85[EUR][1000 genomes]
rs6109918	0.90[EUR][1000 genomes]
rs6109935	0.90[CEU][hapmap];0.91[EUR][1000 genomes]
rs6109946	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6134895	0.90[EUR][1000 genomes]
rs6514411	0.90[EUR][1000 genomes]
rs743183	0.90[CEU][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs910969	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs911014	0.95[CEU][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs932568	0.90[CEU][hapmap];0.85[TSI][hapmap];0.84[EUR][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:63 , 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	chr20:13509000-13528000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr20:13509200-13536200	Weak transcription	Fetal Intestine Large	intestine
19	chr20:13509200-13548200	Weak transcription	Duodenum Mucosa	Duodenum
20	chr20:13509200-13556000	Weak transcription	Fetal Stomach	stomach
21	chr20:13509800-13536200	Weak transcription	Fetal Muscle Leg	muscle
22	chr20:13509800-13538600	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr20:13509800-13547400	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr20:13512800-13548400	Weak transcription	Left Ventricle	heart
25	chr20:13512800-13556000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr20:13513800-13547600	Weak transcription	Primary hematopoietic stem cells	blood
27	chr20:13514000-13532000	Weak transcription	Primary B cells from cord blood	blood
28	chr20:13514000-13536200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr20:13514800-13536600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr20:13514800-13541000	Weak transcription	Primary B cells from peripheral blood	blood
31	chr20:13514800-13546400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr20:13515000-13605600	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr20:13516400-13529000	Weak transcription	Fetal Thymus	thymus
34	chr20:13516600-13528600	Weak transcription	Primary T cells from cord blood	blood
35	chr20:13516600-13538200	Weak transcription	Thymus	Thymus
36	chr20:13524400-13528400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr20:13526200-13527400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr20:13526200-13527400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr20:13526200-13528000	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr20:13526400-13527400	Enhancers	HSMMtube	muscle
41	chr20:13526400-13527800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr20:13526600-13527400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr20:13526600-13527400	Enhancers	Colon Smooth Muscle	Colon
44	chr20:13526600-13527400	Enhancers	Fetal Lung	lung
45	chr20:13526600-13527400	Enhancers	Osteobl	bone
46	chr20:13526800-13527400	Enhancers	Aorta	Aorta
47	chr20:13526800-13527400	Enhancers	Rectal Smooth Muscle	rectum
48	chr20:13526800-13527600	Enhancers	HMEC	breast
49	chr20:13526800-13527800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr20:13526800-13561800	Weak transcription	Stomach Mucosa	stomach

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