Variant report

Variant	rs12542758
Chromosome Location	chr8:99563035-99563036
allele	C/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	MAFK	chr8:99562947-99563037	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr8:99562289..99564114-chr8:99567497..99569189,2	K562	blood:
2	chr8:99561270..99563959-chr8:99566385..99568748,2	MCF-7	breast:
3	chr8:99558108..99560568-chr8:99561487..99563992,2	MCF-7	breast:

Variant related genes	Relation type
STK3	TF binding region
ENSG00000104375	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10755896	0.87[CHB][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10755897	1.00[ASW][hapmap];0.81[CEU][hapmap];0.87[CHB][hapmap];0.95[GIH][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10955186	0.91[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10955187	0.91[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10955188	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10955190	0.82[CHB][hapmap]
rs11774463	0.87[CHB][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap]
rs11775055	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11780292	0.86[EUR][1000 genomes]
rs11780369	0.86[EUR][1000 genomes]
rs11780500	1.00[YRI][hapmap]
rs12542069	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12547297	0.81[CEU][hapmap];0.87[CHB][hapmap];0.82[GIH][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs12549803	0.81[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs12550783	0.81[CEU][hapmap];0.87[CHB][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12677183	0.82[CHB][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12679268	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12680195	0.81[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs12680490	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12680602	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs13258214	0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs13269932	0.82[CHB][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap]
rs13271844	0.80[EUR][1000 genomes]
rs13275915	0.82[CHB][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap]
rs34114299	0.87[CHB][hapmap];0.82[GIH][hapmap];0.81[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35447893	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35798019	0.83[TSI][hapmap]
rs4131873	0.91[ASW][hapmap];0.82[CHB][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.82[YRI][hapmap]
rs4279561	0.82[CHB][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap]
rs4442112	0.87[CHB][hapmap];0.87[CHD][hapmap];0.90[ASN][1000 genomes]
rs4509292	0.81[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4517094	0.82[CHB][hapmap]
rs4549741	0.82[CHB][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap]
rs4734410	0.82[CHB][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap]
rs4735568	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4735569	0.81[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4735570	0.81[CEU][hapmap];0.82[CHB][hapmap];0.95[GIH][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs4735574	0.83[LWK][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.82[YRI][hapmap]
rs57034072	0.85[EUR][1000 genomes]
rs62535381	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62535382	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62535383	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62535404	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62535408	0.86[EUR][1000 genomes]
rs62535410	0.86[EUR][1000 genomes]
rs62535412	0.86[EUR][1000 genomes]
rs6651182	0.87[CHB][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67186645	0.83[ASN][1000 genomes]
rs6992925	0.82[CHB][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap]
rs7016626	0.87[CHB][hapmap];0.85[CHD][hapmap];0.85[ASN][1000 genomes]
rs7818010	0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7838239	1.00[YRI][hapmap]
rs9656842	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1027362	chr8:99469281-99715845	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv539689	chr8:99469281-99715845	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv891218	chr8:99507313-99906221	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv891219	chr8:99526819-99643487	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv611808	chr8:99544765-99591736	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
6	nsv1030498	chr8:99545493-99607093	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12542758	OSR2	cis	cerebellum	SCAN
rs12542758	NCALD	cis	cerebellum	SCAN
rs12542758	FBXO43	cis	parietal	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:99525800-99576400	Weak transcription	Pancreas	Pancrea
2	chr8:99531000-99569600	Weak transcription	HMEC	breast
3	chr8:99531400-99586400	Weak transcription	HSMM	muscle
4	chr8:99533400-99566400	Weak transcription	NHLF	lung
5	chr8:99534600-99567200	Weak transcription	A549	lung
6	chr8:99535400-99571600	Weak transcription	Gastric	stomach
7	chr8:99543000-99566800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr8:99544000-99566800	Weak transcription	Brain Substantia Nigra	brain
9	chr8:99544600-99587000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr8:99546000-99571600	Weak transcription	Fetal Intestine Small	intestine
11	chr8:99546600-99576400	Weak transcription	Primary hematopoietic stem cells	blood
12	chr8:99548600-99569800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr8:99548800-99563400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr8:99549800-99568200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr8:99551400-99566000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr8:99552000-99572600	Weak transcription	Brain Hippocampus Middle	brain
17	chr8:99553400-99569600	Weak transcription	Fetal Lung	lung
18	chr8:99553400-99586000	Weak transcription	Ovary	ovary
19	chr8:99553600-99589600	Weak transcription	Fetal Stomach	stomach
20	chr8:99553800-99566800	Weak transcription	Adipose Nuclei	Adipose
21	chr8:99554200-99567800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr8:99554800-99572800	Weak transcription	Dnd41	blood
23	chr8:99554800-99593200	Weak transcription	K562	blood
24	chr8:99555400-99564000	Weak transcription	Primary T cells from cord blood	blood
25	chr8:99556000-99571600	Weak transcription	Fetal Intestine Large	intestine
26	chr8:99556200-99606200	Weak transcription	Psoas Muscle	Psoas
27	chr8:99557800-99581400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr8:99558800-99564800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr8:99559200-99564400	Weak transcription	NHDF-Ad	bronchial
30	chr8:99559200-99581600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr8:99559600-99569600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr8:99559600-99586200	Weak transcription	Fetal Muscle Trunk	muscle
33	chr8:99559600-99586600	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr8:99559600-99596200	Weak transcription	Colon Smooth Muscle	Colon
35	chr8:99559800-99564400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr8:99559800-99588400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr8:99559800-99601600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr8:99560000-99566200	Weak transcription	HSMMtube	muscle
39	chr8:99560200-99571600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr8:99560200-99586600	Weak transcription	Liver	Liver
41	chr8:99560400-99564800	Weak transcription	GM12878-XiMat	blood
42	chr8:99560400-99568200	Weak transcription	Fetal Muscle Leg	muscle
43	chr8:99560400-99569600	Weak transcription	NHEK	skin
44	chr8:99560400-99586200	Weak transcription	Placenta	Placenta
45	chr8:99560400-99592800	Weak transcription	Left Ventricle	heart
46	chr8:99560400-99593400	Weak transcription	Aorta	Aorta
47	chr8:99560400-99602200	Weak transcription	Monocytes-CD14+_RO01746	blood

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