Variant report

Variant	rs9573578
Chromosome Location	chr13:76104956-76104957
allele	A/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	ARID3A	chr13:76104571-76105292	HepG2	liver:	n/a	n/a
2	POLR2A	chr13:76104715-76106075	K562	blood:	n/a	n/a
3	POLR2A	chr13:76104918-76105131	MCF10A-Er-Src	breast:	n/a	n/a
4	KAP1	chr13:76104341-76105348	U2OS	brain:	n/a	n/a
5	FOXA1	chr13:76104657-76105104	HepG2	liver:	n/a	n/a
6	FOXA2	chr13:76104694-76105072	HepG2	liver:	n/a	n/a
7	JUND	chr13:76104646-76105060	HepG2	liver:	n/a	n/a
8	POLR2A	chr13:76104341-76106613	MCF10A-Er-Src	breast:	n/a	n/a
9	KAP1	chr13:76104702-76105220	HEK293	kidney:	n/a	n/a
10	JUN	chr13:76104701-76105052	HepG2	liver:	n/a	n/a
11	CEBPB	chr13:76104649-76105094	HepG2	liver:	n/a	n/a
12	FOXA1	chr13:76104675-76105220	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:76102775..76109881-chr13:76110381..76113047,9	MCF-7	breast:

Variant related genes	Relation type
COMMD6	TF binding region
ENSG00000188243	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs2031236	0.81[CHB][hapmap];0.82[CHD][hapmap]
rs2296146	0.81[CHB][hapmap];0.82[CHD][hapmap]
rs2328963	0.81[CHB][hapmap]
rs2328964	0.81[CHB][hapmap]
rs3783028	0.81[CHB][hapmap]
rs3818355	0.81[CHB][hapmap];0.82[CHD][hapmap]
rs4611344	0.81[CHB][hapmap]
rs4643195	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4885306	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4885308	1.00[CHB][hapmap];0.83[JPT][hapmap];0.98[ASN][1000 genomes]
rs4885322	0.81[CHB][hapmap];0.84[CHD][hapmap]
rs4885323	0.81[CHB][hapmap]
rs4885324	0.85[CHB][hapmap]
rs55983304	0.87[ASN][1000 genomes]
rs56084319	0.97[ASN][1000 genomes]
rs60497706	0.86[ASN][1000 genomes]
rs6562915	0.81[CHB][hapmap];0.85[CHD][hapmap]
rs6562916	0.81[CHB][hapmap]
rs7317250	0.81[CHB][hapmap];0.82[CHD][hapmap]
rs7321787	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73223948	0.96[ASN][1000 genomes]
rs73223955	0.98[ASN][1000 genomes]
rs7324195	0.81[CHB][hapmap]
rs7339146	0.85[CHB][hapmap]
rs7996884	0.81[CHB][hapmap]
rs8192763	0.81[CHB][hapmap]
rs9543956	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9543957	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9543959	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9543976	0.81[CHB][hapmap];0.82[CHD][hapmap]
rs9543990	0.81[CHB][hapmap]
rs9565177	0.81[CHB][hapmap]
rs9573576	0.91[ASN][1000 genomes]
rs9573577	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[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	esv2761803	chr13:75943309-76161774	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv900562	chr13:76072743-76176680	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv900563	chr13:76093935-76169347	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv900564	chr13:76100090-76156136	Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9573578	COMMD6	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:76093600-76109400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr13:76095600-76109200	Weak transcription	Gastric	stomach
3	chr13:76095800-76111400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr13:76096600-76107400	Weak transcription	Fetal Intestine Small	intestine
5	chr13:76096600-76110400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr13:76096600-76111400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr13:76097000-76111000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr13:76097000-76111600	Weak transcription	Spleen	Spleen
9	chr13:76097400-76106200	Weak transcription	Brain Hippocampus Middle	brain
10	chr13:76097600-76106200	Weak transcription	Fetal Lung	lung
11	chr13:76097600-76107400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr13:76097800-76107200	Weak transcription	Fetal Stomach	stomach
13	chr13:76097800-76110400	Weak transcription	Brain Angular Gyrus	brain
14	chr13:76097800-76110600	Weak transcription	Fetal Brain Male	brain
15	chr13:76097800-76110600	Weak transcription	Fetal Kidney	kidney
16	chr13:76097800-76110600	Weak transcription	Psoas Muscle	Psoas
17	chr13:76097800-76111200	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr13:76098000-76107600	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr13:76098000-76110400	Weak transcription	A549	lung
20	chr13:76098000-76110400	Weak transcription	HUVEC	blood vessel
21	chr13:76098000-76110600	Weak transcription	Brain Anterior Caudate	brain
22	chr13:76098000-76110600	Weak transcription	Rectal Smooth Muscle	rectum
23	chr13:76098000-76111200	Weak transcription	Aorta	Aorta
24	chr13:76098200-76107400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr13:76098200-76107400	Weak transcription	NHLF	lung
26	chr13:76098200-76108200	Weak transcription	NHEK	skin
27	chr13:76098200-76109600	Weak transcription	Brain Germinal Matrix	brain
28	chr13:76098200-76110400	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr13:76098400-76110200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr13:76098600-76111000	Weak transcription	Colonic Mucosa	Colon
31	chr13:76098800-76110400	Weak transcription	Brain Cingulate Gyrus	brain
32	chr13:76098800-76111400	Weak transcription	Esophagus	oesophagus
33	chr13:76099200-76107400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr13:76099400-76109400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr13:76099400-76110400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr13:76099600-76109400	Weak transcription	HSMMtube	muscle
37	chr13:76099600-76110200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr13:76099600-76111000	Weak transcription	K562	blood
39	chr13:76099800-76105000	Strong transcription	HSMM	muscle
40	chr13:76099800-76106400	Weak transcription	Placenta	Placenta
41	chr13:76100000-76105000	Strong transcription	HUES64 Cell Line	embryonic stem cell
42	chr13:76100000-76106200	Weak transcription	Fetal Brain Female	brain
43	chr13:76100000-76107400	Weak transcription	Fetal Muscle Leg	muscle
44	chr13:76100000-76107600	Weak transcription	Fetal Muscle Trunk	muscle
45	chr13:76100000-76109000	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr13:76100000-76109200	Weak transcription	Lung	lung
47	chr13:76100000-76109400	Weak transcription	Left Ventricle	heart
48	chr13:76100000-76109400	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr13:76100000-76110600	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr13:76100000-76111200	Weak transcription	Ovary	ovary

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