Variant report

Variant	rs10163112
Chromosome Location	chr15:76015397-76015398
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	POLR2A	chr15:76015393-76015398	MCF10A-Er-Src	breast:	n/a	n/a
2	JUN	chr15:76015341-76016687	K562	blood:	n/a	chr15:76016330-76016343 chr15:76016331-76016340

Variant related genes	Relation type
ODF3L1	TF binding region

Extended variants
information (count: 77 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10519109	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11852712	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11854305	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11858818	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12101948	0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs12898509	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12899163	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12899303	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12900007	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12900167	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12903661	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12904654	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12905062	0.81[CEU][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12905730	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13329104	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1838939	0.86[YRI][hapmap];0.85[ASN][1000 genomes]
rs1996302	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1996303	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2002668	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2004631	0.83[ASN][1000 genomes]
rs2004920	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2009508	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2017312	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2028948	0.85[ASN][1000 genomes]
rs2290484	0.87[CEU][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2405718	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2405719	0.86[AMR][1000 genomes]
rs2405882	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28404806	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28541422	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28615348	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28651447	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28657001	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28688252	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28695212	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28695716	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28744558	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28833005	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28837134	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34402412	0.95[EUR][1000 genomes]
rs34469290	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34571038	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34605750	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34611707	1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34941412	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34951369	0.83[ASN][1000 genomes]
rs35019194	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35135316	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35136767	0.81[AMR][1000 genomes]
rs35147271	0.84[AMR][1000 genomes]
rs35411779	0.81[EUR][1000 genomes]
rs35745834	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35842909	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs36057011	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4503758	1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4886742	0.81[ASN][1000 genomes]
rs55744943	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs57905971	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs60214227	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67908345	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs71403504	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7163633	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7165531	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7181595	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs74026532	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8026234	0.86[CEU][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8027311	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8028002	1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531901	chr15:75600108-76019966	Genic enhancers Flanking Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
2	esv3445070	chr15:75623136-76045948	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
3	nsv1048028	chr15:75637515-76019967	Strong transcription Genic enhancers Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	161 gene(s)	inside rSNPs	diseases
4	nsv542436	chr15:75637515-76019967	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	161 gene(s)	inside rSNPs	diseases
5	nsv531903	chr15:75889302-76342128	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
6	nsv527186	chr15:75924443-76107730	Active TSS Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	69 gene(s)	inside rSNPs	diseases
7	nsv904392	chr15:75930757-76039262	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
8	nsv904394	chr15:75948671-76039262	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
9	nsv904396	chr15:75961518-76071105	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10163112	ARID3B	cis	cerebellum	SCAN
rs10163112	UBE2Q2	cis	cerebellum	SCAN
rs10163112	FBXO22	cis	parietal	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76005600-76016000	Weak transcription	Aorta	Aorta
2	chr15:76008200-76016000	Weak transcription	Gastric	stomach
3	chr15:76009400-76017600	Enhancers	Stomach Mucosa	stomach
4	chr15:76010000-76015600	Weak transcription	Left Ventricle	heart
5	chr15:76010200-76015800	Weak transcription	Adipose Nuclei	Adipose
6	chr15:76010800-76015600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr15:76011200-76015600	Weak transcription	NH-A	brain
8	chr15:76011200-76015800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr15:76011200-76015800	Weak transcription	Osteobl	bone
10	chr15:76011200-76016000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr15:76011400-76015600	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr15:76011400-76015800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr15:76011400-76016000	Weak transcription	HSMMtube	muscle
14	chr15:76011600-76015600	Weak transcription	NHLF	lung
15	chr15:76011600-76016000	Weak transcription	Ovary	ovary
16	chr15:76011600-76016000	Weak transcription	NHDF-Ad	bronchial
17	chr15:76013000-76018600	Enhancers	Fetal Muscle Leg	muscle
18	chr15:76013200-76016000	Enhancers	Rectal Mucosa Donor 29	rectum
19	chr15:76013200-76017800	Enhancers	Fetal Stomach	stomach
20	chr15:76013400-76015800	Enhancers	Colonic Mucosa	Colon
21	chr15:76013400-76017200	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr15:76013600-76015600	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr15:76013600-76015600	Weak transcription	Brain Germinal Matrix	brain
24	chr15:76013600-76015800	Weak transcription	Fetal Brain Male	brain
25	chr15:76013600-76016000	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr15:76013600-76025000	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr15:76013800-76015400	Weak transcription	Placenta	Placenta
28	chr15:76013800-76015600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr15:76013800-76015600	Weak transcription	Right Atrium	heart
30	chr15:76013800-76015600	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr15:76013800-76015800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr15:76013800-76015800	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr15:76013800-76015800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr15:76013800-76016000	Weak transcription	Liver	Liver
35	chr15:76013800-76016000	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr15:76013800-76016000	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr15:76013800-76016000	Weak transcription	GM12878-XiMat	blood
38	chr15:76013800-76029800	Weak transcription	HSMM	muscle
39	chr15:76014000-76015400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr15:76014000-76015600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr15:76014000-76015600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr15:76014000-76015600	Weak transcription	Esophagus	oesophagus
43	chr15:76014000-76015600	Weak transcription	Fetal Heart	heart
44	chr15:76014000-76015600	Weak transcription	Lung	lung
45	chr15:76014000-76015600	Weak transcription	Right Ventricle	heart
46	chr15:76014000-76015600	Weak transcription	HMEC	breast
47	chr15:76014000-76015600	Weak transcription	K562	blood
48	chr15:76014000-76016000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr15:76014000-76016000	Weak transcription	Brain Angular Gyrus	brain
50	chr15:76014200-76018800	Bivalent Enhancer	Fetal Muscle Trunk	muscle

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