Variant report

Variant	rs13159076
Chromosome Location	chr5:112611314-112611315
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	chr5:112611052..112612599-chr5:112628891..112631844,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171444	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11738528	0.82[ASW][hapmap]
rs1867324	0.82[ASW][hapmap]
rs2120349	0.91[ASW][hapmap]
rs2416309	0.81[CHD][hapmap]
rs637634	0.82[ASW][hapmap];0.90[LWK][hapmap];0.84[MEX][hapmap];0.98[MKK][hapmap];0.81[AFR][1000 genomes]
rs7717906	0.81[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv599396	chr5:112408944-112853189	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv882718	chr5:112519471-112674376	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv882719	chr5:112568212-112706511	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1024747	chr5:112592710-112679373	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13159076	YTHDC2	cis	cerebellum	SCAN
rs13159076	MANBA	trans	cerebellum	SCAN
rs13159076	YTHDC2	cis	parietal	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112586600-112623600	Weak transcription	Pancreas	Pancrea
2	chr5:112587600-112617000	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr5:112600200-112618000	Weak transcription	Fetal Kidney	kidney
4	chr5:112601000-112612400	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr5:112602200-112616600	Weak transcription	Brain Hippocampus Middle	brain
6	chr5:112603000-112611800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr5:112603000-112616800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr5:112603800-112612200	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr5:112604400-112612600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr5:112604600-112612600	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr5:112605000-112611400	Enhancers	HUVEC	blood vessel
12	chr5:112605400-112612400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr5:112606600-112614000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr5:112607200-112614400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr5:112607600-112611600	Weak transcription	Right Atrium	heart
16	chr5:112607600-112616200	Weak transcription	Esophagus	oesophagus
17	chr5:112608000-112628200	Weak transcription	HMEC	breast
18	chr5:112608200-112611400	Enhancers	Adipose Nuclei	Adipose
19	chr5:112608200-112612200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr5:112608400-112612000	Enhancers	H1 Cell Line	embryonic stem cell
21	chr5:112608400-112612000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr5:112608400-112612200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr5:112608600-112612000	Enhancers	Brain Germinal Matrix	brain
24	chr5:112608600-112612400	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr5:112608800-112612200	Enhancers	HUES6 Cell Line	embryonic stem cell
26	chr5:112609000-112612000	Enhancers	Fetal Brain Male	brain
27	chr5:112609000-112612200	Enhancers	Ovary	ovary
28	chr5:112609200-112612400	Enhancers	Fetal Heart	heart
29	chr5:112609600-112611400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr5:112609600-112612000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr5:112609600-112612000	Enhancers	Right Ventricle	heart
32	chr5:112609600-112612600	Enhancers	Left Ventricle	heart
33	chr5:112609600-112614800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr5:112610000-112628200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr5:112610400-112611400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr5:112610400-112611800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
37	chr5:112610400-112612200	Enhancers	H9 Cell Line	embryonic stem cell
38	chr5:112610600-112611400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr5:112610600-112611600	Enhancers	Fetal Brain Female	brain
40	chr5:112610600-112612000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr5:112610600-112612000	Enhancers	Fetal Muscle Leg	muscle
42	chr5:112610600-112612000	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr5:112610600-112612000	Enhancers	Stomach Smooth Muscle	stomach
44	chr5:112610600-112612000	Enhancers	HSMMtube	muscle
45	chr5:112610600-112612200	Enhancers	Liver	Liver
46	chr5:112610800-112611600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr5:112610800-112612000	Enhancers	Breast Myoepithelial Primary Cells	Breast
48	chr5:112610800-112616400	Weak transcription	Spleen	Spleen
49	chr5:112610800-112623200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr5:112611000-112611400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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