Variant report

Variant	rs12506514
Chromosome Location	chr4:7518112-7518113
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:7512552..7515805-chr4:7517576..7521782,4	MCF-7	breast:
2	chr4:7516846..7519696-chr4:7521879..7524111,2	K562	blood:

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11730684	1.00[CHD][hapmap]
rs13117257	1.00[MEX][hapmap]
rs4689131	1.00[CHD][hapmap];0.81[GIH][hapmap]
rs4689767	0.82[GIH][hapmap]
rs4689768	1.00[CHD][hapmap]
rs744356	1.00[CHD][hapmap];1.00[MEX][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7656523	0.84[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.81[MEX][hapmap]
rs7685329	0.84[CEU][hapmap]
rs7688464	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7688472	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916610	chr4:7238883-7731946	Bivalent Enhancer Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
2	nsv593569	chr4:7291363-7626136	Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1011547	chr4:7318232-7637410	Active TSS ZNF genes & repeats Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
4	nsv537017	chr4:7318232-7637410	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
5	nsv469758	chr4:7370083-7546250	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
6	nsv878561	chr4:7402284-7544610	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
7	nsv878563	chr4:7420785-7529367	Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
8	nsv878564	chr4:7421007-7535214	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
9	nsv878566	chr4:7456717-7529367	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region miRNA	1 gene(s)	inside rSNPs	diseases
10	nsv878567	chr4:7456717-7544610	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
11	nsv878568	chr4:7490246-7529367	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
12	nsv878569	chr4:7496857-7544610	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12506514	MRFAP1	cis	cerebellum	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7513800-7518400	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr4:7513800-7518400	Weak transcription	Fetal Brain Female	brain
3	chr4:7514600-7518600	Enhancers	Spleen	Spleen
4	chr4:7515600-7518200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr4:7515600-7519000	Enhancers	Right Ventricle	heart
6	chr4:7515800-7518800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr4:7515800-7520000	Weak transcription	Brain Germinal Matrix	brain
8	chr4:7515800-7522000	Enhancers	Fetal Heart	heart
9	chr4:7516400-7518800	Enhancers	Brain Inferior Temporal Lobe	brain
10	chr4:7516600-7520400	Enhancers	Ovary	ovary
11	chr4:7516800-7518200	Enhancers	Brain Cingulate Gyrus	brain
12	chr4:7517000-7518600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr4:7517000-7518800	Enhancers	Brain Anterior Caudate	brain
14	chr4:7517000-7518800	Bivalent Enhancer	Fetal Muscle Leg	muscle
15	chr4:7517000-7519000	Bivalent Enhancer	Fetal Stomach	stomach
16	chr4:7517200-7518200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr4:7517200-7518200	Flanking Active TSS	Liver	Liver
18	chr4:7517200-7518800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
19	chr4:7517200-7520200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr4:7517200-7520400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr4:7517400-7518200	Enhancers	Stomach Smooth Muscle	stomach
22	chr4:7517400-7518400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr4:7517400-7518400	Enhancers	Adipose Nuclei	Adipose
24	chr4:7517400-7518400	Weak transcription	Pancreas	Pancrea
25	chr4:7517400-7518400	Weak transcription	Right Atrium	heart
26	chr4:7517400-7518600	Flanking Bivalent TSS/Enh	HepG2	liver
27	chr4:7517400-7519000	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr4:7517400-7519000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr4:7517400-7519000	Enhancers	HUES6 Cell Line	embryonic stem cell
30	chr4:7517400-7520000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr4:7517400-7520200	Weak transcription	Brain Angular Gyrus	brain
32	chr4:7517600-7518400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr4:7517600-7518600	Enhancers	Lung	lung
34	chr4:7517600-7519000	Enhancers	Fetal Kidney	kidney
35	chr4:7517800-7518200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr4:7517800-7518200	Enhancers	Colon Smooth Muscle	Colon
37	chr4:7517800-7518400	Bivalent Enhancer	Fetal Lung	lung
38	chr4:7517800-7518800	Enhancers	H1 Cell Line	embryonic stem cell
39	chr4:7517800-7518800	Enhancers	Placenta Amnion	Placenta Amnion
40	chr4:7517800-7520200	Weak transcription	Brain Substantia Nigra	brain
41	chr4:7518000-7518600	Bivalent Enhancer	Placenta	Placenta
42	chr4:7518000-7519000	Enhancers	iPS-18 Cell Line	embryonic stem cell
43	chr4:7518000-7519000	Enhancers	Left Ventricle	heart
44	chr4:7518000-7520000	Weak transcription	Brain Hippocampus Middle	brain

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