Variant report

Variant	rs6040561
Chromosome Location	chr20:11331314-11331315
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr20:11331260-11331410	NHDF-neo	bronchial:	n/a	n/a
2	CEBPB	chr20:11331007-11331375	ECC-1	luminal epithelium:	n/a	chr20:11331222-11331234 chr20:11331151-11331160 chr20:11331149-11331160 chr20:11331151-11331160 chr20:11331151-11331160
3	POLR2A	chr20:11330619-11331345	H1-neurons	neurons:	n/a	n/a
4	STAT3	chr20:11331005-11331618	MCF10A-Er-Src	breast:	n/a	n/a
5	CEBPB	chr20:11330938-11331422	Hela-S3	cervix:	n/a	chr20:11331222-11331234 chr20:11331151-11331160 chr20:11331149-11331160 chr20:11331151-11331160 chr20:11331151-11331160
6	CTCF	chr20:11331260-11331410	HMEC	breast:	n/a	n/a
7	CEBPB	chr20:11330839-11331403	MCF-7	breast:	n/a	chr20:11331222-11331234 chr20:11331151-11331160 chr20:11331149-11331160 chr20:11331151-11331160 chr20:11331151-11331160
8	FOS	chr20:11331045-11331399	MCF10A-Er-Src	breast:	n/a	n/a
9	CEBPB	chr20:11330771-11331570	A549	lung:	n/a	chr20:11331222-11331234 chr20:11331151-11331160 chr20:11331149-11331160 chr20:11331151-11331160 chr20:11331151-11331160
10	CEBPB	chr20:11330965-11331343	HepG2	liver:	n/a	chr20:11331222-11331234 chr20:11331151-11331160 chr20:11331149-11331160 chr20:11331151-11331160 chr20:11331151-11331160
11	MYC	chr20:11330957-11331553	MCF10A-Er-Src	breast:	n/a	n/a
12	CEBPB	chr20:11330960-11331367	A549	lung:	n/a	chr20:11331222-11331234 chr20:11331151-11331160 chr20:11331149-11331160 chr20:11331151-11331160 chr20:11331151-11331160
13	STAT3	chr20:11331005-11331416	MCF10A-Er-Src	breast:	n/a	n/a
14	E2F4	chr20:11330929-11331323	MCF10A-Er-Src	breast:	n/a	n/a
15	CEBPB	chr20:11330984-11331336	H1-hESC	embryonic stem cell:	n/a	chr20:11331222-11331234 chr20:11331151-11331160 chr20:11331149-11331160 chr20:11331151-11331160 chr20:11331151-11331160
16	CEBPB	chr20:11330932-11331397	ECC-1	luminal epithelium:	n/a	chr20:11331222-11331234 chr20:11331151-11331160 chr20:11331149-11331160 chr20:11331151-11331160 chr20:11331151-11331160
17	CTCF	chr20:11331180-11331330	RPTEC	kidney:	n/a	n/a
18	CEBPB	chr20:11330897-11331389	A549	lung:	n/a	chr20:11331222-11331234 chr20:11331151-11331160 chr20:11331149-11331160 chr20:11331151-11331160 chr20:11331151-11331160
19	FOS	chr20:11330938-11331572	MCF10A-Er-Src	breast:	n/a	n/a
20	CTCF	chr20:11331298-11331612	IMR90	lung:	n/a	n/a
21	CEBPB	chr20:11330951-11331521	IMR90	lung:	n/a	chr20:11331222-11331234 chr20:11331151-11331160 chr20:11331149-11331160 chr20:11331151-11331160 chr20:11331151-11331160
22	EP300	chr20:11330982-11331323	Hela-S3	cervix:	n/a	chr20:11331165-11331179
23	MYC	chr20:11331022-11331593	MCF10A-Er-Src	breast:	n/a	n/a
24	CTCF	chr20:11331220-11331370	NHLF	lung:	n/a	n/a
25	FOS	chr20:11330889-11331622	MCF10A-Er-Src	breast:	n/a	n/a
26	CTCF	chr20:11331240-11331390	RPTEC	kidney:	n/a	n/a
27	REST	chr20:11330520-11332657	H1-neurons	neurons:	n/a	n/a
28	POLR2A	chr20:11330947-11331489	MCF10A-Er-Src	breast:	n/a	n/a
29	STAT3	chr20:11330948-11331540	MCF10A-Er-Src	breast:	n/a	n/a
30	STAT3	chr20:11330923-11331400	MCF10A-Er-Src	breast:	n/a	n/a
31	FOS	chr20:11330864-11331503	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:11330194..11333067-chr20:11363546..11365974,2	MCF-7	breast:

Variant related genes	Relation type
RPS11P1	TF binding region

Extended variants
information (count: 14 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs16992379	0.90[AFR][1000 genomes]
rs17261812	0.81[CEU][hapmap]
rs2207111	0.95[AFR][1000 genomes]
rs6033115	0.92[AFR][1000 genomes]
rs6040535	0.81[AFR][1000 genomes]
rs6040544	0.92[AFR][1000 genomes]
rs6040547	0.92[AFR][1000 genomes]
rs6040549	0.88[AFR][1000 genomes]
rs6040550	0.94[AFR][1000 genomes]
rs6040552	0.91[AFR][1000 genomes]
rs6040560	0.95[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065969	chr20:10850562-11464172	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv544181	chr20:10850562-11464172	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv585415	chr20:11134907-11383327	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:11329000-11332000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr20:11330400-11332000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr20:11330400-11332400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr20:11330400-11332600	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr20:11330600-11331400	Enhancers	Fetal Intestine Large	intestine
6	chr20:11330600-11331600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr20:11330600-11331600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr20:11330600-11332200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr20:11330600-11332400	Enhancers	HMEC	breast
10	chr20:11330600-11333400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr20:11330600-11334400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr20:11330800-11331400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr20:11330800-11331400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr20:11330800-11331400	Enhancers	Adipose Nuclei	Adipose
15	chr20:11330800-11331400	Enhancers	Brain Anterior Caudate	brain
16	chr20:11330800-11331400	Enhancers	Hela-S3	cervix
17	chr20:11330800-11331400	Flanking Active TSS	NHEK	skin
18	chr20:11330800-11331600	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr20:11330800-11331600	Enhancers	Duodenum Smooth Muscle	Duodenum
20	chr20:11330800-11331600	Enhancers	Fetal Lung	lung
21	chr20:11330800-11331800	Enhancers	Stomach Mucosa	stomach
22	chr20:11330800-11332000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr20:11330800-11332400	Enhancers	Brain Substantia Nigra	brain
24	chr20:11330800-11333200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr20:11330800-11333600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr20:11330800-11334200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr20:11330800-11336200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr20:11331000-11331400	Enhancers	A549	lung
29	chr20:11331000-11331400	Enhancers	Monocytes-CD14+_RO01746	blood
30	chr20:11331000-11331800	Enhancers	Brain Germinal Matrix	brain
31	chr20:11331000-11331800	Enhancers	Rectal Mucosa Donor 31	rectum
32	chr20:11331000-11332400	Enhancers	Psoas Muscle	Psoas
33	chr20:11331000-11333000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr20:11331000-11338400	Enhancers	Cortex derived primary cultured neurospheres	brain
35	chr20:11331200-11332200	Enhancers	Brain Hippocampus Middle	brain
36	chr20:11331200-11332400	Enhancers	Brain Inferior Temporal Lobe	brain
37	chr20:11331200-11332800	Enhancers	Fetal Intestine Small	intestine
38	chr20:11331200-11333200	Enhancers	iPS-18 Cell Line	embryonic stem cell
39	chr20:11331200-11333800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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