Variant report

Variant	rs6042264
Chromosome Location	chr20:13611315-13611316
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	chr20:13608491..13611413-chr20:13619029..13620797,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000089123	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1040756	0.86[ASN][1000 genomes]
rs11087055	0.82[ASN][1000 genomes]
rs13040087	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2057259	0.88[ASN][1000 genomes]
rs2070307	0.84[AFR][1000 genomes]
rs2070308	0.84[AFR][1000 genomes]
rs2180569	0.88[ASN][1000 genomes]
rs2295503	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2295504	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2327793	0.85[ASN][1000 genomes]
rs2423729	0.83[AFR][1000 genomes]
rs2423731	0.81[AFR][1000 genomes]
rs2423732	0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2423733	0.91[ASN][1000 genomes]
rs2423734	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2423736	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2423737	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2423738	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2423739	0.85[ASN][1000 genomes]
rs34146992	0.92[ASN][1000 genomes]
rs34822601	0.82[ASN][1000 genomes]
rs4303776	0.81[ASN][1000 genomes]
rs4441543	0.84[ASN][1000 genomes]
rs6033766	0.93[ASN][1000 genomes]
rs6033767	0.95[ASN][1000 genomes]
rs6033768	0.93[ASN][1000 genomes]
rs6033773	0.80[AFR][1000 genomes]
rs6033783	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6033793	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6033795	0.89[ASN][1000 genomes]
rs6042225	0.91[ASN][1000 genomes]
rs6042235	0.83[ASN][1000 genomes]
rs6042236	0.93[ASN][1000 genomes]
rs6042239	0.93[ASN][1000 genomes]
rs6042240	0.92[ASN][1000 genomes]
rs6042263	0.84[AFR][1000 genomes]
rs6042266	0.82[AFR][1000 genomes]
rs6042273	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6042285	0.86[ASN][1000 genomes]
rs6042301	0.82[ASN][1000 genomes]
rs6105137	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6105142	0.81[AFR][1000 genomes]
rs6109979	0.80[AFR][1000 genomes]
rs6109983	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6109990	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6109993	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6109995	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6131499	0.83[ASN][1000 genomes]
rs6134919	0.87[ASN][1000 genomes]
rs6134930	0.93[ASN][1000 genomes]
rs6134935	0.93[ASN][1000 genomes]
rs6134948	0.90[ASN][1000 genomes]
rs6514418	0.86[AFR][1000 genomes];0.90[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	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	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
6	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
7	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
8	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

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13526800-13613800	Weak transcription	Hela-S3	cervix
2	chr20:13556200-13618800	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr20:13563800-13619000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr20:13564000-13612400	Weak transcription	Pancreas	Pancrea
5	chr20:13567200-13618600	Weak transcription	Adipose Nuclei	Adipose
6	chr20:13584000-13617800	Weak transcription	Aorta	Aorta
7	chr20:13587000-13618000	Weak transcription	Fetal Brain Male	brain
8	chr20:13588000-13618600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr20:13590800-13617800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr20:13591200-13619000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr20:13592200-13617800	Weak transcription	Small Intestine	intestine
12	chr20:13594400-13618600	Weak transcription	Brain Cingulate Gyrus	brain
13	chr20:13595400-13618200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr20:13595600-13618200	Weak transcription	Colon Smooth Muscle	Colon
15	chr20:13596200-13618200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr20:13596600-13618000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr20:13597400-13618800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr20:13598200-13618800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr20:13599000-13618600	Weak transcription	Fetal Intestine Small	intestine
20	chr20:13601000-13618400	Weak transcription	NHLF	lung
21	chr20:13601400-13611400	Weak transcription	Brain Substantia Nigra	brain
22	chr20:13601600-13618200	Weak transcription	Brain Germinal Matrix	brain
23	chr20:13602000-13618200	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr20:13603200-13618000	Weak transcription	Fetal Kidney	kidney
25	chr20:13603400-13613600	Genic enhancers	Dnd41	blood
26	chr20:13603400-13618000	Weak transcription	A549	lung
27	chr20:13603600-13618600	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr20:13605800-13618800	Weak transcription	Colonic Mucosa	Colon
29	chr20:13605800-13619000	Weak transcription	Spleen	Spleen
30	chr20:13606400-13612000	Weak transcription	Ovary	ovary
31	chr20:13606400-13618200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr20:13606600-13612400	Weak transcription	Lung	lung
33	chr20:13606800-13618200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr20:13607000-13618800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr20:13607400-13618800	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr20:13607600-13618800	Weak transcription	Placenta	Placenta
37	chr20:13607800-13618400	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr20:13608200-13618400	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr20:13608800-13612000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr20:13608800-13612000	Weak transcription	Osteobl	bone
41	chr20:13608800-13613800	Weak transcription	Gastric	stomach
42	chr20:13608800-13618400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr20:13608800-13618600	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr20:13608800-13618800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr20:13608800-13618800	Weak transcription	HSMM	muscle
46	chr20:13609000-13613400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr20:13609000-13618000	Weak transcription	NHEK	skin
48	chr20:13609000-13618200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr20:13609000-13618800	Weak transcription	HSMMtube	muscle
50	chr20:13609200-13617800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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