Variant report

Variant	rs12542069
Chromosome Location	chr8:99569735-99569736
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:99568406..99571836-chr8:99575589..99579865,3	K562	blood:
2	chr8:99567325..99572845-chr8:99952617..99957549,5	MCF-7	breast:
3	chr8:99569567..99570631-chr8:99717657..99718318,3	MCF-7	breast:
4	chr8:99568854..99571836-chr8:99577056..99579865,2	K562	blood:

Variant related genes	Relation type
ENSG00000104375	Chromatin interaction
ENSG00000164920	Chromatin interaction
ENSG00000271930	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10755896	0.85[ASW][hapmap];0.83[CHB][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10755897	0.85[CEU][hapmap];0.83[CHB][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10955186	1.00[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10955187	1.00[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.80[MKK][hapmap];0.95[TSI][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10955188	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11774463	0.83[CHB][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap]
rs11775055	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11778767	0.81[TSI][hapmap]
rs11780292	0.86[EUR][1000 genomes]
rs11780369	0.86[EUR][1000 genomes]
rs12542022	0.82[JPT][hapmap]
rs12542758	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	0.85[CEU][hapmap];0.83[CHB][hapmap];0.82[GIH][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs12549803	0.85[CEU][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs12550783	1.00[ASW][hapmap];0.85[CEU][hapmap];0.83[CHB][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12677183	1.00[ASW][hapmap];0.82[JPT][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.88[TSI][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12679268	0.80[EUR][1000 genomes]
rs12680195	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs12680490	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12680602	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs13258214	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13269932	0.96[LWK][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.94[YRI][hapmap]
rs13271844	0.80[EUR][1000 genomes]
rs13275915	0.91[MEX][hapmap];0.83[TSI][hapmap]
rs16897061	0.82[JPT][hapmap]
rs34114299	0.85[ASW][hapmap];0.83[CHB][hapmap];0.82[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34366206	0.82[GIH][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap]
rs35447893	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35798019	0.83[TSI][hapmap]
rs4131873	0.91[MEX][hapmap];0.88[TSI][hapmap]
rs4279561	0.91[MEX][hapmap];0.83[TSI][hapmap]
rs4370499	0.82[JPT][hapmap]
rs4442112	0.91[CHB][hapmap];0.91[CHD][hapmap];0.82[JPT][hapmap];0.92[ASN][1000 genomes]
rs4509292	0.85[CEU][hapmap];0.83[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4549741	0.91[MEX][hapmap];0.83[TSI][hapmap]
rs4734410	0.93[ASW][hapmap];0.82[JPT][hapmap];0.96[LWK][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.88[TSI][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes]
rs4735568	1.00[ASW][hapmap];0.85[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];0.93[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4735569	0.85[CEU][hapmap];0.83[CHB][hapmap];0.82[JPT][hapmap];0.83[YRI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4735570	1.00[ASW][hapmap];0.85[CEU][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs4735574	0.91[MEX][hapmap];0.83[TSI][hapmap]
rs57034072	0.85[EUR][1000 genomes]
rs62535381	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62535382	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62535383	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62535404	0.83[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	0.83[CHB][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.88[TSI][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs67186645	0.85[ASN][1000 genomes]
rs6992925	0.81[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.94[YRI][hapmap]
rs7016626	0.91[CHB][hapmap];0.89[CHD][hapmap];0.82[JPT][hapmap];0.83[LWK][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs7818010	0.91[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9656842	0.85[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];0.83[YRI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12542069	FBXO43	cis	parietal	SCAN
rs12542069	NCALD	cis	cerebellum	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:99525800-99576400	Weak transcription	Pancreas	Pancrea
2	chr8:99531400-99586400	Weak transcription	HSMM	muscle
3	chr8:99535400-99571600	Weak transcription	Gastric	stomach
4	chr8:99544600-99587000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr8:99546000-99571600	Weak transcription	Fetal Intestine Small	intestine
6	chr8:99546600-99576400	Weak transcription	Primary hematopoietic stem cells	blood
7	chr8:99548600-99569800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr8:99552000-99572600	Weak transcription	Brain Hippocampus Middle	brain
9	chr8:99553400-99586000	Weak transcription	Ovary	ovary
10	chr8:99553600-99589600	Weak transcription	Fetal Stomach	stomach
11	chr8:99554800-99572800	Weak transcription	Dnd41	blood
12	chr8:99554800-99593200	Weak transcription	K562	blood
13	chr8:99556000-99571600	Weak transcription	Fetal Intestine Large	intestine
14	chr8:99556200-99606200	Weak transcription	Psoas Muscle	Psoas
15	chr8:99557800-99581400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr8:99559200-99581600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr8:99559600-99586200	Weak transcription	Fetal Muscle Trunk	muscle
18	chr8:99559600-99586600	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr8:99559600-99596200	Weak transcription	Colon Smooth Muscle	Colon
20	chr8:99559800-99588400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr8:99559800-99601600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr8:99560200-99571600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr8:99560200-99586600	Weak transcription	Liver	Liver
24	chr8:99560400-99586200	Weak transcription	Placenta	Placenta
25	chr8:99560400-99592800	Weak transcription	Left Ventricle	heart
26	chr8:99560400-99593400	Weak transcription	Aorta	Aorta
27	chr8:99560400-99602200	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr8:99566800-99573000	Enhancers	NHDF-Ad	bronchial
29	chr8:99567000-99571000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr8:99568400-99570200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr8:99568600-99570000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr8:99568600-99571400	Weak transcription	Osteobl	bone
33	chr8:99568600-99572200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr8:99568800-99571600	Weak transcription	Adipose Nuclei	Adipose
35	chr8:99569000-99570000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr8:99569000-99570000	Weak transcription	NHLF	lung
37	chr8:99569600-99569800	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr8:99569600-99570200	Enhancers	Fetal Lung	lung
39	chr8:99569600-99570400	Enhancers	HMEC	breast
40	chr8:99569600-99570800	Enhancers	NHEK	skin

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