Variant report

Variant	rs6925839
Chromosome Location	chr6:71303462-71303463
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	chr6:71295996..71298551-chr6:71301722..71304064,2	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10945236	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1140297	0.99[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12190556	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12198920	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12205103	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12215765	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13199529	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs13206086	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13213357	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs13437371	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13654	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1534050	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1917344	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2347427	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2691505	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2691506	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2747703	0.82[EUR][1000 genomes]
rs34378057	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34873840	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35516318	0.82[EUR][1000 genomes]
rs35542509	0.84[ASN][1000 genomes]
rs3763251	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6455371	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6925112	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7341224	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7739098	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7756652	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9446271	0.99[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9446272	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9446273	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9446274	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9446275	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9455133	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9455173	0.99[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9455179	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9455180	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9455185	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9455186	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs998986	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932111	chr6:70736835-71633094	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1027049	chr6:70961610-71561488	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv524328	chr6:70961833-71558805	Flanking Bivalent TSS/Enh Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv917312	chr6:70961903-71601688	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv886145	chr6:71119524-71317480	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv886146	chr6:71219464-71317480	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
7	nsv886147	chr6:71273253-71471863	Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6925839	C6orf57	cis	Thyroid	GTEx
rs6925839	C6orf57	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:71277200-71310600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:71278000-71305200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr6:71278200-71308800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr6:71278600-71308800	Weak transcription	Dnd41	blood
5	chr6:71286000-71304800	Weak transcription	Gastric	stomach
6	chr6:71286200-71310600	Weak transcription	Right Ventricle	heart
7	chr6:71288400-71309800	Weak transcription	Spleen	Spleen
8	chr6:71289800-71310200	Weak transcription	Colonic Mucosa	Colon
9	chr6:71291400-71307800	Weak transcription	Brain Cingulate Gyrus	brain
10	chr6:71291600-71304800	Weak transcription	Brain Angular Gyrus	brain
11	chr6:71291600-71310000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr6:71292400-71304600	Weak transcription	Brain Germinal Matrix	brain
13	chr6:71292600-71305800	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr6:71292600-71310000	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr6:71295000-71304400	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr6:71295400-71305000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr6:71295400-71308800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr6:71295400-71314000	Weak transcription	Aorta	Aorta
19	chr6:71295800-71306200	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr6:71295800-71307200	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr6:71295800-71309000	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr6:71296200-71303800	Weak transcription	Fetal Intestine Large	intestine
23	chr6:71296200-71304400	Weak transcription	Primary hematopoietic stem cells	blood
24	chr6:71296200-71310600	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr6:71298000-71304400	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr6:71298000-71310800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr6:71300600-71303800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr6:71300600-71304200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr6:71300800-71304200	Weak transcription	Fetal Muscle Leg	muscle
30	chr6:71300800-71304600	Weak transcription	Brain Hippocampus Middle	brain
31	chr6:71300800-71305400	Weak transcription	Brain Anterior Caudate	brain
32	chr6:71300800-71310200	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr6:71301000-71304800	Weak transcription	Liver	Liver
34	chr6:71301000-71304800	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr6:71301000-71309600	Weak transcription	Ovary	ovary
36	chr6:71301000-71310000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr6:71301200-71306400	Weak transcription	Primary B cells from cord blood	blood
38	chr6:71301200-71308800	Weak transcription	Primary T cells from cord blood	blood
39	chr6:71301200-71309800	Weak transcription	Stomach Smooth Muscle	stomach
40	chr6:71301800-71303600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr6:71303000-71308800	Weak transcription	Fetal Stomach	stomach
42	chr6:71303200-71303800	Weak transcription	Lung	lung
43	chr6:71303400-71303600	Weak transcription	Fetal Intestine Small	intestine
44	chr6:71303400-71304200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr6:71303400-71305200	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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