Variant report

Variant	rs12510308
Chromosome Location	chr4:129149880-129149881
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:129148539..129151049-chr4:129208191..129211640,3	MCF-7	breast:
2	chr4:129148695..129150886-chr4:129155942..129157749,2	MCF-7	breast:
3	chr4:129148431..129150686-chr4:129162614..129165468,2	MCF-7	breast:
4	chr4:129149417..129151058-chr4:129208924..129211039,2	K562	blood:
5	chr4:129142342..129144660-chr4:129149158..129151312,2	MCF-7	breast:
6	chr4:129147470..129151366-chr4:129195142..129198204,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164040	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10002814	0.92[ASN][1000 genomes]
rs11098951	0.83[EUR][1000 genomes]
rs11733374	0.86[ASN][1000 genomes]
rs11737026	0.81[EUR][1000 genomes]
rs12498291	0.81[EUR][1000 genomes]
rs12505763	0.81[CHD][hapmap];0.95[JPT][hapmap]
rs12511648	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13103695	0.86[ASN][1000 genomes]
rs1403125	0.86[ASN][1000 genomes]
rs1522432	0.86[ASN][1000 genomes]
rs1809796	0.80[EUR][1000 genomes]
rs1851400	0.82[ASN][1000 genomes]
rs1948506	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2140107	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2204117	0.81[EUR][1000 genomes]
rs34174952	0.86[ASN][1000 genomes]
rs35053204	0.85[AFR][1000 genomes]
rs4383632	0.80[LWK][hapmap]
rs4624668	0.86[ASN][1000 genomes]
rs4975220	0.89[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs4975299	0.88[EUR][1000 genomes]
rs4975300	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6534670	0.80[LWK][hapmap]
rs6534672	0.80[CEU][hapmap];0.82[GIH][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs6534673	0.80[CEU][hapmap];0.80[EUR][1000 genomes]
rs6534674	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6534675	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6849865	0.81[EUR][1000 genomes]
rs7667562	0.80[CEU][hapmap]
rs7679633	0.86[ASN][1000 genomes]
rs7688852	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7691103	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879915	chr4:128167093-129150590	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	esv3390887	chr4:128932563-129207255	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12510308	MFSD8	cis	cerebellum	SCAN
rs12510308	LARP2	cis	multi-tissue	Pritchard

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:129144200-129151400	Weak transcription	Lung	lung
2	chr4:129145000-129150000	Weak transcription	Fetal Intestine Small	intestine
3	chr4:129148800-129150000	Enhancers	HSMM	muscle
4	chr4:129148800-129151000	Enhancers	Muscle Satellite Cultured Cells	--
5	chr4:129148800-129151000	Enhancers	Osteobl	bone
6	chr4:129149000-129150000	Enhancers	HSMMtube	muscle
7	chr4:129149000-129150400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr4:129149000-129150400	Enhancers	Fetal Muscle Leg	muscle
9	chr4:129149000-129150600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr4:129149000-129150600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr4:129149000-129150800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr4:129149000-129150800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr4:129149000-129151000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr4:129149000-129151000	Enhancers	Placenta Amnion	Placenta Amnion
15	chr4:129149000-129151200	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr4:129149000-129151200	Enhancers	NHDF-Ad	bronchial
17	chr4:129149200-129150000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr4:129149200-129150400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr4:129149200-129150600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr4:129149200-129151000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr4:129149200-129151000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr4:129149400-129150400	Enhancers	Brain Hippocampus Middle	brain
23	chr4:129149400-129150600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr4:129149400-129150800	Enhancers	NH-A	brain
25	chr4:129149600-129150000	Weak transcription	NHLF	lung
26	chr4:129149800-129150000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr4:129149800-129150000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr4:129149800-129150200	Weak transcription	Fetal Heart	heart
29	chr4:129149800-129150600	Enhancers	Brain Germinal Matrix	brain
30	chr4:129149800-129150600	Active TSS	Pancreatic Islets	Pancreatic Islet
31	chr4:129149800-129150800	Weak transcription	HMEC	breast
32	chr4:129149800-129151400	Weak transcription	Placenta	Placenta
33	chr4:129149800-129152000	Weak transcription	NHEK	skin
34	chr4:129149800-129161800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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