Variant report

Variant	rs13211088
Chromosome Location	chr6:163749552-163749553
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	chr6:163742095..163749894-chr6:163832230..163837162,13	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112531	Chromatin interaction
ENSG00000270419	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11752722	0.87[ASN][1000 genomes]
rs12195744	0.88[JPT][hapmap]
rs12527711	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12529440	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13190955	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13196281	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13211237	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13214515	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13218916	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17393817	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34418608	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56167893	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56212042	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6921139	0.97[ASN][1000 genomes]
rs6925566	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6928196	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs71569403	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9458808	0.92[CEU][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9458809	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932127	chr6:163000261-163950870	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1022610	chr6:163591786-163814041	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv605188	chr6:163697439-163772096	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv534621	chr6:163731741-163950870	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	esv3391848	chr6:163748791-163752416	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
6	esv1803546	chr6:163749552-163757127	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13211088	QKI	cis	parietal	SCAN
rs13211088	LOC441177	cis	parietal	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:163732000-163749600	Weak transcription	Spleen	Spleen
2	chr6:163743400-163749600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:163744200-163751000	Weak transcription	Right Atrium	heart
4	chr6:163745000-163753200	Weak transcription	Right Ventricle	heart
5	chr6:163745200-163767000	Enhancers	Brain Inferior Temporal Lobe	brain
6	chr6:163745600-163773600	Enhancers	Brain Substantia Nigra	brain
7	chr6:163745800-163754000	Enhancers	Brain Angular Gyrus	brain
8	chr6:163746400-163755200	Weak transcription	Psoas Muscle	Psoas
9	chr6:163746600-163750800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr6:163746600-163750800	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr6:163746600-163750800	Weak transcription	Adipose Nuclei	Adipose
12	chr6:163746600-163750800	Weak transcription	NH-A	brain
13	chr6:163746600-163751000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr6:163746600-163751200	Weak transcription	Fetal Heart	heart
15	chr6:163746600-163753400	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr6:163746600-163759400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:163746600-163759800	Enhancers	Brain Anterior Caudate	brain
18	chr6:163746600-163759800	Enhancers	Brain Hippocampus Middle	brain
19	chr6:163746600-163764400	Enhancers	Brain Cingulate Gyrus	brain
20	chr6:163746800-163751000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr6:163746800-163751000	Weak transcription	HSMM	muscle
22	chr6:163746800-163754200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr6:163747400-163750800	Weak transcription	A549	lung
24	chr6:163748600-163749800	Enhancers	Left Ventricle	heart
25	chr6:163748600-163752400	Enhancers	Fetal Muscle Leg	muscle
26	chr6:163748600-163756600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
27	chr6:163748800-163749800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr6:163748800-163750200	Enhancers	Fetal Muscle Trunk	muscle
29	chr6:163748800-163750800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr6:163749400-163749600	Enhancers	HUES6 Cell Line	embryonic stem cell
31	chr6:163749400-163750000	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr6:163749400-163750000	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr6:163749400-163751000	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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