Variant report

Variant	rs749977
Chromosome Location	chr5:116275461-116275462
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:116274317..116277091-chr5:116277592..116280132,2	MCF-7	breast:

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11742262	0.90[ASN][1000 genomes]
rs17311978	0.86[ASN][1000 genomes]
rs2416457	0.91[EUR][1000 genomes]
rs4920862	0.96[ASN][1000 genomes]
rs4920863	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59419128	0.90[ASN][1000 genomes]
rs6897938	0.90[ASN][1000 genomes]
rs779139	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv527974	chr5:115987168-116303678	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv462403	chr5:115994775-116284378	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv599485	chr5:115994775-116284378	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1030056	chr5:116008971-116278725	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1033140	chr5:116035131-116314673	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1020292	chr5:116183712-116349633	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1033379	chr5:116244963-116464338	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv882750	chr5:116252792-116292091	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
9	esv2760934	chr5:116261466-116280605	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv1017455	chr5:116261466-116302129	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs749977	ATG12	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:116272600-116275600	Enhancers	Right Ventricle	heart
2	chr5:116272800-116275600	Enhancers	Left Ventricle	heart
3	chr5:116273000-116276800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr5:116273000-116276800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr5:116273400-116275600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr5:116273800-116277400	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr5:116274000-116275600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr5:116274000-116276200	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr5:116274000-116276800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr5:116274200-116275600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr5:116274200-116275600	Enhancers	Fetal Heart	heart
12	chr5:116274200-116276000	Enhancers	Brain Cingulate Gyrus	brain
13	chr5:116274200-116276000	Enhancers	Brain Hippocampus Middle	brain
14	chr5:116274200-116276200	Enhancers	Fetal Muscle Leg	muscle
15	chr5:116274400-116275600	Enhancers	Brain Anterior Caudate	brain
16	chr5:116274600-116275600	Enhancers	Brain Inferior Temporal Lobe	brain
17	chr5:116274600-116276000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
18	chr5:116274600-116276000	Enhancers	H1 Cell Line	embryonic stem cell
19	chr5:116274600-116278400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr5:116274800-116275600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr5:116275000-116275600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr5:116275000-116275600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr5:116275000-116275800	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr5:116275000-116277600	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr5:116275000-116277600	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr5:116275000-116280600	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr5:116275200-116278200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr5:116275200-116278400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr5:116275200-116279600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr5:116275400-116275600	Active TSS	HSMMtube	muscle
31	chr5:116275400-116275800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr5:116275400-116276000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell

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