Variant report

Variant	rs9455186
Chromosome Location	chr6:71304887-71304888
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	POLR2A	chr6:71304840-71304968	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
ENSG00000271967	TF binding region

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10945236	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1140297	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1208476	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1208477	0.82[EUR][1000 genomes]
rs12190556	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12198920	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12205103	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12215765	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13199529	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13206086	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13213357	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13437371	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13654	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1534050	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1917344	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2347427	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2691505	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2691506	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2747703	0.84[EUR][1000 genomes]
rs34378057	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34873840	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35516318	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35542509	0.85[ASN][1000 genomes]
rs3763251	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6455371	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6925112	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6925839	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7341224	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7739098	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7756652	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9446271	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9446272	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9446273	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9446274	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9446275	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9455133	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9455173	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9455179	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9455180	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9455185	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs998986	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[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
rs9455186	C6orf57	cis	Thyroid	GTEx
rs9455186	C6orf57	cis	lung	GTEx

Chromatin state (count:28 , 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	chr6:71286200-71310600	Weak transcription	Right Ventricle	heart
6	chr6:71288400-71309800	Weak transcription	Spleen	Spleen
7	chr6:71289800-71310200	Weak transcription	Colonic Mucosa	Colon
8	chr6:71291400-71307800	Weak transcription	Brain Cingulate Gyrus	brain
9	chr6:71291600-71310000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr6:71292600-71305800	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr6:71292600-71310000	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr6:71295400-71305000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr6:71295400-71308800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr6:71295400-71314000	Weak transcription	Aorta	Aorta
15	chr6:71295800-71306200	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr6:71295800-71307200	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr6:71295800-71309000	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr6:71296200-71310600	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr6:71298000-71310800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr6:71300800-71305400	Weak transcription	Brain Anterior Caudate	brain
21	chr6:71300800-71310200	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr6:71301000-71309600	Weak transcription	Ovary	ovary
23	chr6:71301000-71310000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr6:71301200-71306400	Weak transcription	Primary B cells from cord blood	blood
25	chr6:71301200-71308800	Weak transcription	Primary T cells from cord blood	blood
26	chr6:71301200-71309800	Weak transcription	Stomach Smooth Muscle	stomach
27	chr6:71303000-71308800	Weak transcription	Fetal Stomach	stomach
28	chr6:71303400-71305200	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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