Variant report

Variant	rs6042258
Chromosome Location	chr20:13602433-13602434
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:13601399..13603374-chr20:13617085..13619673,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000089123	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11697938	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11699618	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2423735	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2423740	1.00[CEU][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2423741	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2423742	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2423743	0.83[ASN][1000 genomes]
rs6033751	1.00[CEU][hapmap]
rs6033770	1.00[CEU][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6033792	0.83[ASN][1000 genomes]
rs6033799	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6042171	1.00[CEU][hapmap]
rs6042232	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6042297	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6042302	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7266705	1.00[EUR][1000 genomes]
rs73899353	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73899363	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	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
3	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
4	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
5	esv1797514	chr20:13541011-13610424	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv1061323	chr20:13551004-13746346	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	nsv912689	chr20:13570331-14155881	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv531478	chr20:13580524-13814797	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv1059221	chr20:13589432-13977327	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer 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	11 gene(s)	inside rSNPs	diseases
10	nsv962558	chr20:13595511-13605918	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13515000-13605600	Weak transcription	Primary T helper cells PMA-I stimulated	--
2	chr20:13526800-13613800	Weak transcription	Hela-S3	cervix
3	chr20:13535600-13608000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr20:13556200-13618800	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr20:13563800-13619000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr20:13564000-13602600	Weak transcription	Ovary	ovary
7	chr20:13564000-13612400	Weak transcription	Pancreas	Pancrea
8	chr20:13564200-13602800	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr20:13564200-13608400	Weak transcription	HSMM	muscle
10	chr20:13567200-13608600	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr20:13567200-13618600	Weak transcription	Adipose Nuclei	Adipose
12	chr20:13567400-13602800	Weak transcription	A549	lung
13	chr20:13567400-13606400	Weak transcription	Primary B cells from peripheral blood	blood
14	chr20:13567400-13608400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr20:13567400-13608400	Weak transcription	HMEC	breast
16	chr20:13567600-13608600	Weak transcription	Fetal Muscle Trunk	muscle
17	chr20:13568000-13608400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr20:13568400-13607200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr20:13568800-13602800	Weak transcription	Fetal Intestine Large	intestine
20	chr20:13572000-13607800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr20:13573600-13609400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr20:13574200-13606600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr20:13574400-13606400	Weak transcription	Thymus	Thymus
24	chr20:13574600-13606600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr20:13581200-13606200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr20:13582000-13603000	Weak transcription	Liver	Liver
27	chr20:13582200-13606200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr20:13582600-13608000	Weak transcription	HSMMtube	muscle
29	chr20:13583200-13602800	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr20:13583200-13607200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr20:13583200-13607200	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr20:13583400-13607000	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr20:13583800-13605400	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr20:13584000-13617800	Weak transcription	Aorta	Aorta
35	chr20:13585000-13610600	Weak transcription	Psoas Muscle	Psoas
36	chr20:13585200-13602800	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr20:13585200-13609000	Weak transcription	Fetal Muscle Leg	muscle
38	chr20:13585600-13606400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr20:13586600-13608600	Weak transcription	GM12878-XiMat	blood
40	chr20:13587000-13606400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr20:13587000-13618000	Weak transcription	Fetal Brain Male	brain
42	chr20:13588000-13618600	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr20:13588600-13609200	Weak transcription	Left Ventricle	heart
44	chr20:13589400-13602600	Weak transcription	Primary B cells from cord blood	blood
45	chr20:13589400-13603000	Genic enhancers	Dnd41	blood
46	chr20:13589600-13602600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr20:13589600-13603000	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr20:13589800-13608400	Weak transcription	Osteobl	bone
49	chr20:13590800-13617800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr20:13591200-13619000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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