Variant report

Variant	rs9493454
Chromosome Location	chr6:133144629-133144630
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:133142358..133145641-chr6:133228438..133230524,3	K562	blood:
2	chr6:133093368..133095334-chr6:133141299..133145047,3	K562	blood:
3	chr6:133144384..133146734-chr6:134279858..134281420,2	K562	blood:
4	chr6:133143184..133145778-chr6:133351555..133353623,2	K562	blood:
5	chr6:133140672..133145394-chr6:133829879..133833202,4	K562	blood:
6	chr6:133083233..133085227-chr6:133144108..133145647,2	K562	blood:
7	chr6:132860709..132862896-chr6:133144372..133146096,2	K562	blood:
8	chr6:133143807..133144760-chr6:133833610..133834401,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000112303	Chromatin interaction
ENSG00000238059	Chromatin interaction
ENSG00000227954	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10457596	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10484629	1.00[CEU][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11962883	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11964512	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12193474	0.91[TSI][hapmap]
rs12198849	0.92[ASN][1000 genomes]
rs12203977	0.82[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12204027	1.00[CEU][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12211701	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1467403	1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1467404	0.88[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3813347	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58832890	0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61421874	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62424539	0.92[ASN][1000 genomes]
rs6569847	1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6569848	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6910639	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6912936	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6915168	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6934161	1.00[CEU][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73554431	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7738071	0.82[ASW][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7738400	1.00[JPT][hapmap]
rs7758703	0.88[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7761365	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7765224	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7769051	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7770081	0.88[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9321367	0.88[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9321371	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9399041	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9493435	0.88[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9493436	1.00[JPT][hapmap]
rs9493437	1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9493438	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9493443	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9493444	0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9493445	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9493446	1.00[CEU][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532069	chr6:132776411-133462292	Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv1015742	chr6:132933666-133285852	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
3	nsv886676	chr6:133111706-133168582	Flanking Active TSS Genic enhancers Enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
4	esv1806734	chr6:133125643-133168582	Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9493454	C6orf192	Cis_1M	lymphoblastoid	RTeQTL
rs9493454	C6orf192	cis	multi-tissue	Pritchard

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:133137200-133145400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:133139400-133146400	Weak transcription	Psoas Muscle	Psoas
3	chr6:133139600-133145400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr6:133139800-133145400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr6:133140800-133153800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:133141200-133145600	Weak transcription	Liver	Liver
7	chr6:133141200-133145600	Weak transcription	HepG2	liver
8	chr6:133141400-133145400	Weak transcription	Primary hematopoietic stem cells	blood
9	chr6:133141400-133145400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr6:133141400-133145400	Weak transcription	Brain Hippocampus Middle	brain
11	chr6:133141400-133145400	Weak transcription	Colon Smooth Muscle	Colon
12	chr6:133141400-133145400	Weak transcription	Small Intestine	intestine
13	chr6:133141400-133145600	Weak transcription	Adipose Nuclei	Adipose
14	chr6:133141400-133151800	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr6:133142200-133145400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr6:133142400-133146600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr6:133142600-133145200	Weak transcription	K562	blood
18	chr6:133144000-133145800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr6:133144200-133144800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr6:133144200-133144800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr6:133144200-133144800	Enhancers	Primary T killer memory cells from peripheral blood	blood
22	chr6:133144200-133145400	Enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr6:133144200-133145400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr6:133144400-133145200	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr6:133144600-133145600	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr6:133144600-133146600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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