Variant report

Variant	rs9573580
Chromosome Location	chr13:76111280-76111281
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:76102775..76109881-chr13:76110381..76113047,9	MCF-7	breast:
2	chr13:76055919..76057695-chr13:76110507..76112437,2	MCF-7	breast:
3	chr13:76101020..76103303-chr13:76108939..76111291,2	K562	blood:
4	chr13:76109717..76113590-chr13:76122029..76126081,5	MCF-7	breast:
5	chr13:76109113..76111805-chr13:76112674..76114626,2	K562	blood:
6	chr13:76055248..76057886-chr13:76110224..76112780,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000118939	Chromatin interaction
ENSG00000261553	Chromatin interaction
ENSG00000188243	Chromatin interaction
ENSG00000136111	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1080346	0.88[ASN][1000 genomes]
rs1080347	0.88[ASN][1000 genomes]
rs12866456	0.81[CEU][hapmap];0.84[CHB][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap]
rs1323694	0.95[CHB][hapmap];0.86[ASN][1000 genomes]
rs1323696	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs1408042	0.88[ASN][1000 genomes]
rs1535728	0.95[CHB][hapmap];0.98[CHD][hapmap];0.86[ASN][1000 genomes]
rs2031235	0.80[CEU][hapmap];0.84[CHB][hapmap];0.81[JPT][hapmap]
rs2281762	0.84[CHB][hapmap]
rs2328961	0.84[CHB][hapmap]
rs2328962	0.81[CEU][hapmap];0.84[CHB][hapmap];0.84[GIH][hapmap]
rs2876705	0.95[CHB][hapmap];0.98[CHD][hapmap];0.84[ASN][1000 genomes]
rs3812844	0.84[CHB][hapmap]
rs3812845	0.81[CEU][hapmap];0.84[CHB][hapmap]
rs3812846	0.81[CEU][hapmap];0.84[CHB][hapmap];0.84[GIH][hapmap]
rs4539477	0.81[JPT][hapmap]
rs4884008	0.81[CEU][hapmap];0.84[CHB][hapmap];0.81[JPT][hapmap]
rs4885319	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs4885321	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs6562903	0.88[ASN][1000 genomes]
rs7139862	0.81[CEU][hapmap];0.84[CHB][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap]
rs7319227	0.88[ASN][1000 genomes]
rs7319334	0.94[CHB][hapmap];0.95[CHD][hapmap];0.88[ASN][1000 genomes]
rs7326807	0.84[CHB][hapmap]
rs7358977	0.81[CEU][hapmap];0.84[CHB][hapmap]
rs7982613	0.84[CHB][hapmap]
rs7984443	0.84[CHB][hapmap]
rs7995040	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs8000062	0.83[CHB][hapmap]
rs8192741	0.81[CEU][hapmap];0.84[CHB][hapmap];0.81[JPT][hapmap]
rs8192746	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs9318358	0.81[CEU][hapmap];0.84[GIH][hapmap]
rs9530453	0.84[CHB][hapmap]
rs9543951	0.83[ASN][1000 genomes]
rs9543966	0.94[ASN][1000 genomes]
rs9543969	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9543970	0.95[ASN][1000 genomes]
rs9543971	0.93[ASN][1000 genomes]
rs9543994	0.84[CHB][hapmap]
rs966058	0.81[CEU][hapmap];0.84[CHB][hapmap];0.81[JPT][hapmap]
rs972542	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:17 , 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
5	esv3326553	chr13:76106251-76120849	Active TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	esv3346687	chr13:76106451-76115149	Flanking Active TSS Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	esv3363843	chr13:76106551-76113949	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	esv14404	chr13:76107773-76119573	Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	esv2596575	chr13:76109159-76111338	Genic enhancers Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
10	esv1833250	chr13:76109534-76117768	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv442676	chr13:76109534-76117768	Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
12	esv2760289	chr13:76109536-76117768	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
13	nsv514711	chr13:76111087-76115423	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
14	esv2421984	chr13:76111280-76119506	Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
15	nsv525594	chr13:76111280-76119506	Weak transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
16	nsv818980	chr13:76111280-76119506	Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
17	nsv900565	chr13:76111280-76169347	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9573580	COMMD6	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:76095800-76111400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr13:76096600-76111400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr13:76097000-76111600	Weak transcription	Spleen	Spleen
4	chr13:76098800-76111400	Weak transcription	Esophagus	oesophagus
5	chr13:76109200-76111400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr13:76109600-76111400	Weak transcription	Left Ventricle	heart
7	chr13:76109800-76111400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr13:76109800-76111400	Weak transcription	Gastric	stomach
9	chr13:76109800-76111400	Weak transcription	Lung	lung
10	chr13:76110000-76111400	Enhancers	Small Intestine	intestine
11	chr13:76110200-76111400	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr13:76110400-76111400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
13	chr13:76110400-76111400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
14	chr13:76110400-76111400	Flanking Active TSS	Osteobl	bone
15	chr13:76110400-76111600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr13:76110400-76112800	Active TSS	Rectal Mucosa Donor 29	rectum
17	chr13:76110600-76111400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr13:76110600-76111400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
19	chr13:76110600-76111400	Flanking Active TSS	Brain Anterior Caudate	brain
20	chr13:76110600-76111400	Flanking Active TSS	Brain Germinal Matrix	brain
21	chr13:76110600-76111400	Flanking Active TSS	Duodenum Mucosa	Duodenum
22	chr13:76110600-76111400	Enhancers	Pancreas	Pancrea
23	chr13:76110600-76111400	Flanking Active TSS	HepG2	liver
24	chr13:76110600-76111600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
25	chr13:76110600-76111800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
26	chr13:76110600-76111800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr13:76110600-76111800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr13:76110600-76112600	Active TSS	H9 Cell Line	embryonic stem cell
29	chr13:76110800-76111400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr13:76110800-76111400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr13:76110800-76111400	Flanking Active TSS	Brain Hippocampus Middle	brain
32	chr13:76110800-76111400	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
33	chr13:76110800-76111400	Flanking Active TSS	Dnd41	blood
34	chr13:76110800-76111400	Flanking Active TSS	NHEK	skin
35	chr13:76110800-76111600	Flanking Active TSS	Primary T cells from cord blood	blood
36	chr13:76110800-76111600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
37	chr13:76110800-76111800	Flanking Active TSS	Primary B cells from cord blood	blood
38	chr13:76110800-76111800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
39	chr13:76110800-76112400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
40	chr13:76110800-76112400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr13:76110800-76112600	Active TSS	H1 Cell Line	embryonic stem cell
42	chr13:76110800-76112600	Active TSS	iPS-20b Cell Line	embryonic stem cell
43	chr13:76110800-76112600	Active TSS	Psoas Muscle	Psoas
44	chr13:76110800-76112600	Active TSS	NHDF-Ad	bronchial
45	chr13:76110800-76112800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr13:76110800-76112800	Active TSS	HUES48 Cell Line	embryonic stem cell
47	chr13:76110800-76112800	Active TSS	HUES64 Cell Line	embryonic stem cell
48	chr13:76110800-76112800	Active TSS	GM12878-XiMat	blood
49	chr13:76111000-76111400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
50	chr13:76111000-76111400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain

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