Variant report

Variant	rs6042672
Chromosome Location	chr20:14306896-14306897
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: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11087084	0.81[CEU][hapmap];0.87[CHB][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs204629	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs204636	0.81[GIH][hapmap]
rs204637	0.84[MEX][hapmap]
rs204645	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2208456	0.88[CHB][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.80[TSI][hapmap]
rs2327847	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6033952	0.84[EUR][1000 genomes]
rs6105243	0.88[CHB][hapmap];0.93[GIH][hapmap];0.83[TSI][hapmap]
rs6105246	0.83[CEU][hapmap];0.88[CHB][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6105247	0.83[CEU][hapmap];0.88[CHB][hapmap];0.90[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.80[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6110235	0.82[CHB][hapmap]
rs6110242	0.82[CHB][hapmap]
rs6110247	0.88[CHB][hapmap]
rs8126410	0.82[CHB][hapmap]

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:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:14294800-14314000	Weak transcription	Rectal Smooth Muscle	rectum
2	chr20:14296000-14312000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr20:14303600-14307000	Genic enhancers	HMEC	breast
4	chr20:14303600-14308200	Strong transcription	Fetal Kidney	kidney
5	chr20:14303600-14323400	Weak transcription	Small Intestine	intestine
6	chr20:14304000-14308200	Strong transcription	Duodenum Mucosa	Duodenum
7	chr20:14304000-14313600	Weak transcription	Fetal Brain Male	brain
8	chr20:14304000-14315600	Weak transcription	HSMMtube	muscle
9	chr20:14304200-14310400	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr20:14304200-14311000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr20:14304600-14309400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr20:14304600-14311800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr20:14304800-14314400	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr20:14305200-14317200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr20:14305400-14307400	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr20:14305400-14309600	Strong transcription	Liver	Liver
17	chr20:14305400-14314400	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr20:14305600-14307200	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr20:14305800-14317200	Weak transcription	Aorta	Aorta
20	chr20:14306000-14308400	Strong transcription	Cortex derived primary cultured neurospheres	brain
21	chr20:14306000-14310400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr20:14306000-14312800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr20:14306000-14314200	Weak transcription	HSMM	muscle
24	chr20:14306200-14307000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr20:14306200-14307000	Strong transcription	Ovary	ovary
26	chr20:14306200-14307200	Strong transcription	Brain Angular Gyrus	brain
27	chr20:14306200-14307200	Strong transcription	Fetal Lung	lung
28	chr20:14306200-14307400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr20:14306200-14307400	Strong transcription	A549	lung
30	chr20:14306200-14307800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr20:14306200-14307800	Strong transcription	NHLF	lung
32	chr20:14306200-14308000	Strong transcription	Duodenum Smooth Muscle	Duodenum
33	chr20:14306200-14308200	Strong transcription	Brain Cingulate Gyrus	brain
34	chr20:14306200-14308200	Strong transcription	Colon Smooth Muscle	Colon
35	chr20:14306200-14308200	Strong transcription	Fetal Muscle Trunk	muscle
36	chr20:14306200-14308200	Strong transcription	Gastric	stomach
37	chr20:14306200-14309800	Strong transcription	NHEK	skin
38	chr20:14306200-14313600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr20:14306400-14307000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr20:14306400-14307000	Strong transcription	Fetal Intestine Small	intestine
41	chr20:14306400-14307200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr20:14306400-14307400	ZNF genes & repeats	Lung	lung
43	chr20:14306400-14307600	Strong transcription	Pancreatic Islets	Pancreatic Islet
44	chr20:14306400-14307800	Strong transcription	Muscle Satellite Cultured Cells	--
45	chr20:14306400-14307800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr20:14306400-14307800	ZNF genes & repeats	Fetal Muscle Leg	muscle
47	chr20:14306400-14307800	Strong transcription	Placenta Amnion	Placenta Amnion
48	chr20:14306400-14308000	Strong transcription	Fetal Brain Female	brain
49	chr20:14306400-14308200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr20:14306400-14308200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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