Variant report

Variant	rs6870926
Chromosome Location	chr5:178300191-178300192
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:178299499..178302283-chr5:178303072..178304596,2	MCF-7	breast:

Extended variants
information (count: 77 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10039708	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11249599	0.82[EUR][1000 genomes]
rs11948175	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11948664	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11948690	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11949180	1.00[CEU][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11949181	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11949892	1.00[CEU][hapmap];0.88[YRI][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11949941	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11950641	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11950746	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11952790	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11954382	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11955047	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11958804	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11958887	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11958941	1.00[CEU][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11960942	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12186577	1.00[MEX][hapmap];0.95[TSI][hapmap]
rs12186584	1.00[MEX][hapmap];0.95[TSI][hapmap];0.80[EUR][1000 genomes]
rs12187167	1.00[MEX][hapmap];0.95[TSI][hapmap];0.80[EUR][1000 genomes]
rs12553	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1566106	0.92[CEU][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs17664194	1.00[MEX][hapmap];0.87[TSI][hapmap]
rs35609799	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35957383	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56814168	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56872885	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56932649	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56951084	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs57153194	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs57426447	0.90[EUR][1000 genomes]
rs58354049	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58554591	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs58672680	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58679434	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58941917	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs59242428	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59736551	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs59829327	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59849584	0.80[EUR][1000 genomes]
rs59994898	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60178472	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60277514	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60417551	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60601817	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60813042	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61295075	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61310482	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61492890	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61744382	0.80[EUR][1000 genomes]
rs6600991	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6859174	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6861717	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6862829	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs6863160	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6863202	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6863603	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6865216	1.00[CEU][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6866591	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6877663	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6878353	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6882396	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6883566	1.00[CEU][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6887256	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6890083	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6894878	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6895371	1.00[CEU][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7706558	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7724141	0.93[CEU][hapmap]
rs7727497	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7729560	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7729717	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7731067	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[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	nsv883218	chr5:178219855-178349391	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv462574	chr5:178269682-178313078	Genic enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv600463	chr5:178269682-178313078	Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6870926	CNOT6	cis	cerebellum	SCAN
rs6870926	NOP16	cis	parietal	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178287600-178302400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:178288200-178317400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
3	chr5:178288800-178302200	Strong transcription	Skeletal Muscle Male	skeletal muscle
4	chr5:178288800-178317400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr5:178289000-178301000	Strong transcription	Fetal Muscle Leg	muscle
6	chr5:178289000-178301600	Weak transcription	Stomach Mucosa	stomach
7	chr5:178289400-178302200	Strong transcription	Brain Anterior Caudate	brain
8	chr5:178289600-178317400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr5:178289800-178300200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr5:178289800-178300200	Strong transcription	Muscle Satellite Cultured Cells	--
11	chr5:178290000-178302200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr5:178290600-178301200	Strong transcription	Brain Cingulate Gyrus	brain
13	chr5:178290800-178300200	Strong transcription	Left Ventricle	heart
14	chr5:178291200-178317400	ZNF genes & repeats	Liver	Liver
15	chr5:178291400-178300200	Strong transcription	Dnd41	blood
16	chr5:178292000-178303000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr5:178292200-178302200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr5:178292600-178300200	Strong transcription	Primary B cells from peripheral blood	blood
19	chr5:178292600-178300200	Strong transcription	Brain Inferior Temporal Lobe	brain
20	chr5:178292600-178300600	Strong transcription	Rectal Mucosa Donor 31	rectum
21	chr5:178292600-178301200	Strong transcription	Osteobl	bone
22	chr5:178292600-178305000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr5:178292600-178305200	Strong transcription	Stomach Smooth Muscle	stomach
24	chr5:178292800-178301400	Strong transcription	Rectal Smooth Muscle	rectum
25	chr5:178293400-178301000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr5:178294200-178301400	Weak transcription	Hela-S3	cervix
27	chr5:178294800-178300400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr5:178295000-178300400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr5:178296000-178301200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr5:178296000-178305000	ZNF genes & repeats	A549	lung
31	chr5:178296000-178305200	ZNF genes & repeats	Primary B cells from cord blood	blood
32	chr5:178296000-178305400	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
33	chr5:178296000-178319200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
34	chr5:178296200-178315600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
35	chr5:178296200-178319200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr5:178296400-178302400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr5:178296400-178311200	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
38	chr5:178296400-178317600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
39	chr5:178297000-178300600	Weak transcription	Colon Smooth Muscle	Colon
40	chr5:178297000-178301200	Strong transcription	Ovary	ovary
41	chr5:178297200-178315800	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
42	chr5:178297400-178300200	Strong transcription	K562	blood
43	chr5:178297400-178315600	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
44	chr5:178297400-178317400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr5:178297400-178317400	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
46	chr5:178297400-178317400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr5:178297600-178303600	ZNF genes & repeats	NHEK	skin
48	chr5:178297600-178305000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr5:178297600-178305200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
50	chr5:178297600-178317400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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