Variant report

Variant	rs9395504
Chromosome Location	chr6:49494933-49494934
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:49494658..49496334-chr6:49499353..49501283,2	MCF-7	breast:
2	chr6:49487185..49488956-chr6:49492974..49495933,2	K562	blood:
3	chr6:49493967..49496814-chr6:49514614..49516159,2	MCF-7	breast:
4	chr6:49493503..49496187-chr6:49508534..49510793,2	MCF-7	breast:
5	chr6:49493393..49496049-chr6:49496487..49500188,3	K562	blood:
6	chr6:49493637..49498162-chr6:49501160..49505862,5	K562	blood:
7	chr6:49481051..49482766-chr6:49492466..49495213,2	K562	blood:

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1480611	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1480612	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1480613	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1947861	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2061972	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2061973	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2127754	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2498470	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2498471	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2498472	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2501969	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2501970	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2501971	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4715134	0.87[CEU][hapmap];0.94[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6942364	0.89[MEX][hapmap]
rs7739192	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7740682	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7757014	0.91[CEU][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9296618	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9367359	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9369906	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9473582	0.87[CEU][hapmap];0.94[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][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	nsv1024959	chr6:49290141-49652124	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1021136	chr6:49295037-49631278	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv885881	chr6:49439805-49575141	Weak transcription Bivalent Enhancer Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv933942	chr6:49480550-50004231	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9395504	CENPQ	cis	lung	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:49484200-49496000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr6:49489400-49496400	Enhancers	Liver	Liver
3	chr6:49491400-49495400	Enhancers	HepG2	liver
4	chr6:49492400-49496400	Weak transcription	Stomach Mucosa	stomach
5	chr6:49492800-49495800	Weak transcription	NHEK	skin
6	chr6:49494200-49495200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr6:49494200-49495200	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr6:49494200-49495400	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr6:49494400-49495000	Enhancers	Rectal Mucosa Donor 29	rectum
10	chr6:49494400-49495400	Enhancers	H1 Cell Line	embryonic stem cell
11	chr6:49494400-49496200	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr6:49494600-49495200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr6:49494600-49495200	Enhancers	Fetal Intestine Large	intestine
14	chr6:49494600-49495200	Enhancers	Fetal Intestine Small	intestine
15	chr6:49494600-49495400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
16	chr6:49494600-49496200	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr6:49494600-49496400	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr6:49494600-49496600	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr6:49494800-49495200	Enhancers	H9 Cell Line	embryonic stem cell
20	chr6:49494800-49495600	Enhancers	iPS-20b Cell Line	embryonic stem cell
21	chr6:49494800-49496600	Enhancers	ES-I3 Cell Line	embryonic stem cell

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