Variant report

Variant	rs9600487
Chromosome Location	chr13:76104670-76104671
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	KAP1	chr13:76104341-76105348	U2OS	brain:	n/a	n/a
3	FOXA1	chr13:76104657-76105104	HepG2	liver:	n/a	n/a
4	JUND	chr13:76104646-76105060	HepG2	liver:	n/a	n/a
5	POLR2A	chr13:76104341-76106613	MCF10A-Er-Src	breast:	n/a	n/a
6	CEBPB	chr13:76104649-76105094	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: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs2274047	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs2274048	0.85[CHB][hapmap];0.90[GIH][hapmap];0.82[JPT][hapmap]
rs2328949	0.84[ASN][1000 genomes]
rs2328950	0.90[ASN][1000 genomes]
rs34615010	0.93[ASN][1000 genomes]
rs4884005	1.00[ASN][1000 genomes]
rs55742020	0.80[ASN][1000 genomes]
rs7332334	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8192757	0.85[CHB][hapmap];0.90[GIH][hapmap];0.82[JPT][hapmap]
rs8192761	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs9318360	0.90[GIH][hapmap]
rs9530451	0.85[CHB][hapmap];0.90[GIH][hapmap];0.82[JPT][hapmap]
rs9530452	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs9543963	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9543964	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9543967	0.88[ASN][1000 genomes]
rs9543983	0.81[GIH][hapmap]
rs9543986	0.85[CHB][hapmap];0.90[GIH][hapmap];0.82[JPT][hapmap]
rs9543995	0.82[CHB][hapmap]
rs9544001	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs9544003	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs9544006	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs9573582	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs9593088	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9593090	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9593092	0.84[ASN][1000 genomes]
rs9600483	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9600484	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9652173	1.00[CEU][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MKK][hapmap];0.94[TSI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9600487	UCHL3	cis	parietal	SCAN
rs9600487	UCHL3	cis	cerebellum	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:76089000-76104800	Weak transcription	NHDF-Ad	bronchial
2	chr13:76093600-76109400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr13:76095600-76109200	Weak transcription	Gastric	stomach
4	chr13:76095800-76111400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr13:76096600-76107400	Weak transcription	Fetal Intestine Small	intestine
6	chr13:76096600-76110400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr13:76096600-76111400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr13:76097000-76111000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr13:76097000-76111600	Weak transcription	Spleen	Spleen
10	chr13:76097400-76104800	Weak transcription	GM12878-XiMat	blood
11	chr13:76097400-76106200	Weak transcription	Brain Hippocampus Middle	brain
12	chr13:76097600-76106200	Weak transcription	Fetal Lung	lung
13	chr13:76097600-76107400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr13:76097800-76107200	Weak transcription	Fetal Stomach	stomach
15	chr13:76097800-76110400	Weak transcription	Brain Angular Gyrus	brain
16	chr13:76097800-76110600	Weak transcription	Fetal Brain Male	brain
17	chr13:76097800-76110600	Weak transcription	Fetal Kidney	kidney
18	chr13:76097800-76110600	Weak transcription	Psoas Muscle	Psoas
19	chr13:76097800-76111200	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr13:76098000-76107600	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr13:76098000-76110400	Weak transcription	A549	lung
22	chr13:76098000-76110400	Weak transcription	HUVEC	blood vessel
23	chr13:76098000-76110600	Weak transcription	Brain Anterior Caudate	brain
24	chr13:76098000-76110600	Weak transcription	Rectal Smooth Muscle	rectum
25	chr13:76098000-76111200	Weak transcription	Aorta	Aorta
26	chr13:76098200-76107400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr13:76098200-76107400	Weak transcription	NHLF	lung
28	chr13:76098200-76108200	Weak transcription	NHEK	skin
29	chr13:76098200-76109600	Weak transcription	Brain Germinal Matrix	brain
30	chr13:76098200-76110400	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr13:76098400-76110200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr13:76098600-76111000	Weak transcription	Colonic Mucosa	Colon
33	chr13:76098800-76110400	Weak transcription	Brain Cingulate Gyrus	brain
34	chr13:76098800-76111400	Weak transcription	Esophagus	oesophagus
35	chr13:76099200-76107400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr13:76099400-76109400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr13:76099400-76110400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr13:76099600-76109400	Weak transcription	HSMMtube	muscle
39	chr13:76099600-76110200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr13:76099600-76111000	Weak transcription	K562	blood
41	chr13:76099800-76105000	Strong transcription	HSMM	muscle
42	chr13:76099800-76106400	Weak transcription	Placenta	Placenta
43	chr13:76100000-76105000	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr13:76100000-76106200	Weak transcription	Fetal Brain Female	brain
45	chr13:76100000-76107400	Weak transcription	Fetal Muscle Leg	muscle
46	chr13:76100000-76107600	Weak transcription	Fetal Muscle Trunk	muscle
47	chr13:76100000-76109000	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr13:76100000-76109200	Weak transcription	Lung	lung
49	chr13:76100000-76109400	Weak transcription	Left Ventricle	heart
50	chr13:76100000-76109400	Weak transcription	Sigmoid Colon	Sigmoid Colon

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