Variant report

Variant	rs6042671
Chromosome Location	chr20:14305469-14305470
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	chr20:14305353..14307056-chr20:14308528..14310326,2	MCF-7	breast:

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs6033919	1.00[AMR][1000 genomes]
rs6033956	1.00[AMR][1000 genomes]
rs6033974	1.00[AMR][1000 genomes]
rs6042594	1.00[AMR][1000 genomes]
rs6042595	1.00[AMR][1000 genomes]
rs6042663	1.00[AMR][1000 genomes]
rs6042670	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6042690	1.00[AMR][1000 genomes]
rs6042691	1.00[AMR][1000 genomes]
rs6042709	1.00[AMR][1000 genomes]
rs6042716	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv531479	chr20:13632491-14434432	Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv1057486	chr20:14077828-14469129	ZNF genes & repeats Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1066235	chr20:14173771-14389050	Weak transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv458872	chr20:14189779-14317390	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv470540	chr20:14189779-14317390	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer Strong transcription 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	1 gene(s)	inside rSNPs	diseases
7	nsv585439	chr20:14189779-14317390	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv1055499	chr20:14224873-14848061	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv432101	chr20:14294196-14353346	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:14289600-14306400	Weak transcription	Fetal Intestine Small	intestine
2	chr20:14293000-14306200	Weak transcription	Colon Smooth Muscle	Colon
3	chr20:14294800-14306400	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr20:14294800-14314000	Weak transcription	Rectal Smooth Muscle	rectum
5	chr20:14295000-14306000	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr20:14296000-14312000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr20:14299000-14306200	Weak transcription	Fetal Lung	lung
8	chr20:14299200-14306400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr20:14301800-14306400	Weak transcription	Fetal Intestine Large	intestine
10	chr20:14303600-14306000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr20:14303600-14307000	Genic enhancers	HMEC	breast
12	chr20:14303600-14308200	Strong transcription	Fetal Kidney	kidney
13	chr20:14303600-14323400	Weak transcription	Small Intestine	intestine
14	chr20:14303800-14306400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr20:14304000-14306600	Weak transcription	Brain Germinal Matrix	brain
16	chr20:14304000-14308200	Strong transcription	Duodenum Mucosa	Duodenum
17	chr20:14304000-14313600	Weak transcription	Fetal Brain Male	brain
18	chr20:14304000-14315600	Weak transcription	HSMMtube	muscle
19	chr20:14304200-14306400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr20:14304200-14310400	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr20:14304200-14311000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr20:14304400-14306200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr20:14304400-14306800	Weak transcription	Fetal Heart	heart
24	chr20:14304600-14306200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr20:14304600-14306200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr20:14304600-14306200	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr20:14304600-14306200	Weak transcription	Ovary	ovary
28	chr20:14304600-14306200	Weak transcription	A549	lung
29	chr20:14304600-14306200	Weak transcription	NHLF	lung
30	chr20:14304600-14306400	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr20:14304600-14309400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr20:14304600-14311800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr20:14304800-14306200	Weak transcription	Brain Angular Gyrus	brain
34	chr20:14304800-14306200	Weak transcription	Brain Cingulate Gyrus	brain
35	chr20:14304800-14306200	Weak transcription	Gastric	stomach
36	chr20:14304800-14306400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr20:14304800-14306400	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr20:14304800-14306400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr20:14304800-14306400	Weak transcription	Fetal Brain Female	brain
40	chr20:14304800-14306400	Weak transcription	Fetal Stomach	stomach
41	chr20:14304800-14306400	Weak transcription	Pancreas	Pancrea
42	chr20:14304800-14306400	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr20:14304800-14306400	Weak transcription	Stomach Smooth Muscle	stomach
44	chr20:14304800-14314400	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr20:14305000-14306000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr20:14305000-14306600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr20:14305200-14306200	Weak transcription	NHEK	skin
48	chr20:14305200-14306800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr20:14305200-14317200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr20:14305400-14306400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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