Variant report

Variant	rs6565063
Chromosome Location	chr16:82768568-82768569
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	chr16:82762397..82764526-chr16:82767820..82769912,2	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12716952	0.94[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12928133	1.00[CHD][hapmap];0.93[ASN][1000 genomes]
rs12929312	0.85[ASN][1000 genomes]
rs12932668	0.82[CHB][hapmap];0.94[CHD][hapmap];0.87[ASN][1000 genomes]
rs1381508	0.81[ASN][1000 genomes]
rs1381509	0.94[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1381510	0.88[CEU][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1462038	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16958414	0.94[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16958474	0.88[CHD][hapmap];0.89[ASN][1000 genomes]
rs1870847	1.00[CHD][hapmap];0.89[ASN][1000 genomes]
rs35385909	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35764641	0.95[ASN][1000 genomes]
rs7189174	1.00[CHB][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8058967	0.82[CHB][hapmap];0.89[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532599	chr16:82074439-82926863	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
2	nsv573367	chr16:82140561-83040846	Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
3	nsv1057341	chr16:82363800-83198907	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
4	nsv542997	chr16:82363800-83198907	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
5	nsv1059718	chr16:82564054-82810003	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
6	nsv573379	chr16:82713551-82887631	Strong transcription Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
7	nsv907024	chr16:82713874-82768568	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA miRNA	n/a	inside rSNPs	diseases
8	esv2751616	chr16:82714696-82852296	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1 gene(s)	inside rSNPs	diseases
9	nsv907025	chr16:82718030-82768568	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS	Chromatin interactive region lncRNA miRNA	n/a	inside rSNPs	diseases
10	nsv1067216	chr16:82719694-82821762	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1 gene(s)	inside rSNPs	diseases
11	nsv543000	chr16:82719694-82821762	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1 gene(s)	inside rSNPs	diseases
12	nsv1064438	chr16:82762729-82788901	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
13	nsv907026	chr16:82765607-82812853	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6565063	KCNG4	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:82750200-82780600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr16:82762000-82773800	Weak transcription	NHEK	skin
3	chr16:82763400-82768600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr16:82764600-82768600	Weak transcription	NHDF-Ad	bronchial
5	chr16:82765000-82768600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr16:82765400-82768600	Enhancers	Skeletal Muscle Female	skeletal muscle
7	chr16:82766000-82769000	Enhancers	Fetal Heart	heart
8	chr16:82766600-82770600	Enhancers	Aorta	Aorta
9	chr16:82766600-82770600	Enhancers	Left Ventricle	heart
10	chr16:82766800-82769200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr16:82766800-82788600	Weak transcription	HMEC	breast
12	chr16:82767000-82768600	Weak transcription	HSMM	muscle
13	chr16:82767400-82768600	Enhancers	Psoas Muscle	Psoas
14	chr16:82767400-82768800	Enhancers	Stomach Smooth Muscle	stomach
15	chr16:82767400-82770800	Enhancers	Fetal Brain Male	brain
16	chr16:82767600-82768600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr16:82767600-82769400	Enhancers	Right Atrium	heart
18	chr16:82767600-82771000	Enhancers	Fetal Muscle Leg	muscle
19	chr16:82767800-82769200	Enhancers	Adipose Nuclei	Adipose
20	chr16:82767800-82769600	Enhancers	Right Ventricle	heart
21	chr16:82767800-82771000	Enhancers	Fetal Stomach	stomach
22	chr16:82768000-82768600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr16:82768000-82768600	Enhancers	Fetal Muscle Trunk	muscle
24	chr16:82768000-82769000	Enhancers	GM12878-XiMat	blood
25	chr16:82768000-82771200	Enhancers	Brain Germinal Matrix	brain
26	chr16:82768200-82768800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
27	chr16:82768200-82770200	Enhancers	Fetal Brain Female	brain
28	chr16:82768200-82771000	Enhancers	HSMMtube	muscle
29	chr16:82768400-82769000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr16:82768400-82769400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
31	chr16:82768400-82769800	Enhancers	Brain Inferior Temporal Lobe	brain
32	chr16:82768400-82771000	Enhancers	Colon Smooth Muscle	Colon

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