Variant report

Variant	rs10124515
Chromosome Location	chr9:116073892-116073893
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:116068586..116075781-chr9:116167998..116173640,10	MCF-7	breast:
2	chr9:116071329..116074445-chr9:116134233..116136581,3	MCF-7	breast:
3	chr9:116048493..116050036-chr9:116073858..116076574,2	K562	blood:
4	chr9:116072265..116074041-chr9:116171279..116174233,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000148229	Chromatin interaction
ENSG00000157653	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10481674	0.84[LWK][hapmap]
rs10759638	0.81[CHB][hapmap];0.81[LWK][hapmap]
rs10759639	0.81[ASN][1000 genomes]
rs10817476	0.85[CHB][hapmap]
rs10981713	0.86[CHB][hapmap]
rs10981714	0.86[CHB][hapmap]
rs10981715	0.81[CHB][hapmap]
rs10981719	0.86[CHB][hapmap]
rs10981734	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs10981762	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs11789755	0.81[CHB][hapmap]
rs12343629	0.81[CHB][hapmap]
rs12350131	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16932730	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs2093691	0.86[CHB][hapmap];0.84[CHD][hapmap];0.94[JPT][hapmap]
rs2296073	0.86[CHB][hapmap]
rs2296075	0.90[CHB][hapmap];0.82[CHD][hapmap];0.87[ASN][1000 genomes]
rs2418249	0.80[CHB][hapmap]
rs28440160	0.85[ASN][1000 genomes]
rs35772163	0.83[ASN][1000 genomes]
rs3750532	0.81[CHB][hapmap]
rs3750533	0.81[CHB][hapmap]
rs3750534	0.81[CHB][hapmap]
rs4979231	0.81[CHB][hapmap]
rs6478001	0.87[ASN][1000 genomes]
rs6478006	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs71503561	0.80[ASN][1000 genomes]
rs7849513	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs7850003	0.85[ASN][1000 genomes]
rs7860625	0.95[CHB][hapmap];0.92[CHD][hapmap];0.89[JPT][hapmap];0.83[TSI][hapmap];0.85[ASN][1000 genomes]
rs7868271	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs7873862	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530949	chr9:115821128-116487796	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv1042663	chr9:115920158-116167140	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv893744	chr9:115934852-116170227	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10124515	IKBKAP	cis	cerebellum	SCAN
rs10124515	ORM1	cis	cerebellum	SCAN
rs10124515	BSPRY	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116055200-116085200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr9:116056000-116087000	Weak transcription	Thymus	Thymus
3	chr9:116062600-116075600	Weak transcription	Placenta	Placenta
4	chr9:116065400-116086800	Weak transcription	Gastric	stomach
5	chr9:116065600-116079000	Weak transcription	Fetal Intestine Small	intestine
6	chr9:116065600-116083400	Weak transcription	Esophagus	oesophagus
7	chr9:116070000-116080000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr9:116070200-116077400	Weak transcription	Ovary	ovary
9	chr9:116070200-116077800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr9:116070800-116083800	Weak transcription	Spleen	Spleen
11	chr9:116072000-116085200	Weak transcription	Rectal Smooth Muscle	rectum
12	chr9:116072400-116074000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr9:116072400-116074600	Enhancers	Left Ventricle	heart
14	chr9:116072600-116074200	Enhancers	Fetal Heart	heart
15	chr9:116072800-116074600	Weak transcription	Fetal Muscle Trunk	muscle
16	chr9:116072800-116079200	Weak transcription	Lung	lung
17	chr9:116072800-116080200	Weak transcription	Primary hematopoietic stem cells	blood
18	chr9:116073000-116080400	Weak transcription	Colon Smooth Muscle	Colon
19	chr9:116073200-116077200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr9:116073200-116077400	Weak transcription	Fetal Stomach	stomach
21	chr9:116073200-116078400	Weak transcription	Pancreas	Pancrea
22	chr9:116073200-116079600	Weak transcription	Fetal Lung	lung
23	chr9:116073200-116081000	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr9:116073800-116074000	Enhancers	Right Ventricle	heart
25	chr9:116073800-116076200	Enhancers	Fetal Muscle Leg	muscle
26	chr9:116073800-116080000	Weak transcription	Adipose Nuclei	Adipose
27	chr9:116073800-116101600	Weak transcription	Skeletal Muscle Male	skeletal muscle

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