Variant report

Variant	rs3799667
Chromosome Location	chr6:166928011-166928012
allele	C/G
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	RAD21	chr6:166927654-166928119	HCT-116	colon:	n/a	chr6:166927945-166927954 chr6:166927822-166927841
2	SMC3	chr6:166927598-166929040	SK-N-SH	brain:	n/a	chr6:166927823-166927837 chr6:166927823-166927830
3	RCOR1	chr6:166927751-166929314	IMR90	lung:	n/a	n/a
4	CTCF	chr6:166927900-166928050	HepG2	liver:	n/a	chr6:166927943-166927956
5	RAD21	chr6:166927628-166928018	H1-hESC	embryonic stem cell:	n/a	chr6:166927945-166927954 chr6:166927822-166927841
6	RAD21	chr6:166927673-166928014	IMR90	lung:	n/a	chr6:166927945-166927954 chr6:166927822-166927841
7	RAD21	chr6:166927632-166928018	ECC-1	luminal epithelium:	n/a	chr6:166927945-166927954 chr6:166927822-166927841
8	RAD21	chr6:166927596-166928112	H1-hESC	embryonic stem cell:	n/a	chr6:166927945-166927954 chr6:166927822-166927841
9	CTCF	chr6:166927880-166928030	NHLF	lung:	n/a	chr6:166927943-166927956
10	CTCF	chr6:166927980-166928130	BJ	skin:	n/a	n/a
11	RAD21	chr6:166927590-166928085	ECC-1	luminal epithelium:	n/a	chr6:166927945-166927954 chr6:166927822-166927841

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:166869518..166870276-chr6:166927954..166928779,2	MCF-7	breast:

Variant related genes	Relation type
RPS6KA2	TF binding region

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10214537	0.90[EUR][1000 genomes]
rs12528147	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs12528167	0.90[EUR][1000 genomes]
rs35302651	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3757193	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3778418	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3778422	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3799654	0.90[EUR][1000 genomes]
rs3799658	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3799670	0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs55665778	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9457174	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][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	esv3490076	chr6:166727901-167306743	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
2	esv3490077	chr6:166727901-167306743	Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
3	nsv886941	chr6:166907173-166996991	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:166894800-166928400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr6:166899400-166929400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:166901000-166954800	Weak transcription	Rectal Smooth Muscle	rectum
4	chr6:166902200-166954400	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr6:166902600-166952800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr6:166905000-166928200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr6:166905000-166928400	Weak transcription	HSMM	muscle
8	chr6:166909400-166928400	Strong transcription	Muscle Satellite Cultured Cells	--
9	chr6:166909600-166943800	Weak transcription	Colonic Mucosa	Colon
10	chr6:166911200-166928200	Weak transcription	NH-A	brain
11	chr6:166912200-166931200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr6:166913000-166929000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr6:166913000-166952000	Weak transcription	Primary T cells from cord blood	blood
14	chr6:166916200-166954200	Weak transcription	Right Atrium	heart
15	chr6:166916400-166940400	Weak transcription	Fetal Heart	heart
16	chr6:166917200-166932000	Weak transcription	Primary B cells from cord blood	blood
17	chr6:166917800-166928400	Weak transcription	NHEK	skin
18	chr6:166918000-166928200	Weak transcription	Fetal Intestine Small	intestine
19	chr6:166918000-166928600	Weak transcription	HUVEC	blood vessel
20	chr6:166918200-166928600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr6:166918400-166931400	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr6:166919200-166928600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr6:166921200-166930000	Weak transcription	Fetal Intestine Large	intestine
24	chr6:166921400-166930000	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr6:166921400-166930200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr6:166921400-166943600	Weak transcription	Fetal Lung	lung
27	chr6:166921600-166932000	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr6:166921600-166932000	Weak transcription	Fetal Kidney	kidney
29	chr6:166921600-166937400	Weak transcription	Fetal Brain Male	brain
30	chr6:166922400-166928600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr6:166922400-166929400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr6:166923000-166930000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr6:166923000-166930000	Weak transcription	Esophagus	oesophagus
34	chr6:166923000-166931400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr6:166923000-166937200	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr6:166923000-166940400	Weak transcription	Aorta	Aorta
37	chr6:166923000-166943800	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr6:166923200-166928400	Weak transcription	Brain Anterior Caudate	brain
39	chr6:166923200-166928400	Weak transcription	Brain Substantia Nigra	brain
40	chr6:166923200-166931200	Weak transcription	Brain Germinal Matrix	brain
41	chr6:166923200-166932200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr6:166923200-166940200	Weak transcription	Ovary	ovary
43	chr6:166923200-166943200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr6:166923200-166943800	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr6:166923600-166928400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr6:166923600-166928400	Weak transcription	Brain Hippocampus Middle	brain
47	chr6:166923600-166928600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr6:166923600-166936800	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr6:166923800-166930000	Weak transcription	Placenta	Placenta
50	chr6:166923800-166944400	Weak transcription	Psoas Muscle	Psoas

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