Variant report

Variant	rs12553616
Chromosome Location	chr9:92859417-92859418
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:91924753..91927067-chr9:92857901..92860576,2	MCF-7	breast:
2	chr9:92219124..92221595-chr9:92854778..92859945,4	MCF-7	breast:
3	chr9:92219255..92222737-chr9:92856647..92859942,4	MCF-7	breast:
4	chr9:92207554..92215968-chr9:92858794..92866301,17	MCF-7	breast:
5	chr9:92850629..92852906-chr9:92857887..92860130,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000123975	Chromatin interaction
ENSG00000130222	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10122998	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992049	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11790815	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11792422	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12345484	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12346907	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12552603	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12553823	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1329046	0.92[CEU][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16906191	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28718362	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs423239	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7048555	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73651746	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73651747	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[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	nsv482303	chr9:92752928-92890226	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
2	nsv614852	chr9:92786722-93100550	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv893563	chr9:92816727-92967125	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	esv3380801	chr9:92859132-92863030	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12553616	AUH	cis	cerebellum	SCAN
rs12553616	GOLM1	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:92848800-92862200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr9:92855600-92864400	Weak transcription	Brain Cingulate Gyrus	brain
3	chr9:92857000-92860400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
4	chr9:92857000-92861600	Enhancers	Fetal Brain Female	brain
5	chr9:92857000-92862400	Enhancers	Fetal Brain Male	brain
6	chr9:92857800-92859800	Enhancers	Skeletal Muscle Male	skeletal muscle
7	chr9:92857800-92862800	Enhancers	Brain Germinal Matrix	brain
8	chr9:92857800-92862800	Enhancers	Skeletal Muscle Female	skeletal muscle
9	chr9:92858000-92859800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr9:92858000-92860400	Enhancers	Left Ventricle	heart
11	chr9:92858000-92860800	Enhancers	Right Ventricle	heart
12	chr9:92858000-92861200	Bivalent Enhancer	Fetal Muscle Leg	muscle
13	chr9:92858400-92859600	Enhancers	Pancreatic Islets	Pancreatic Islet
14	chr9:92858400-92861000	Weak transcription	Fetal Lung	lung
15	chr9:92858400-92861600	Weak transcription	Pancreas	Pancrea
16	chr9:92858600-92859600	Weak transcription	Psoas Muscle	Psoas
17	chr9:92858600-92870200	Weak transcription	Right Atrium	heart
18	chr9:92858800-92864400	Weak transcription	Fetal Intestine Large	intestine
19	chr9:92859000-92861200	Weak transcription	HSMMtube	muscle
20	chr9:92859400-92859800	Enhancers	Spleen	Spleen

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