Variant report

Variant	rs1348523
Chromosome Location	chr5:179495532-179495533
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:179447593..179449240-chr5:179494400..179496143,2	MCF-7	breast:
2	chr5:179481868..179484254-chr5:179494865..179496879,2	MCF-7	breast:
3	chr5:179494887..179496936-chr5:179502532..179505071,2	MCF-7	breast:
4	chr5:179494847..179497645-chr5:179497864..179501359,4	K562	blood:
5	chr5:179467128..179469131-chr5:179495464..179498336,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000113269	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10041471	0.86[ASN][1000 genomes]
rs10045947	0.88[CEU][hapmap];0.83[LWK][hapmap];0.97[MKK][hapmap]
rs10073876	0.94[CEU][hapmap]
rs10075114	0.90[ASN][1000 genomes]
rs10075627	0.88[CEU][hapmap]
rs11954181	0.94[CEU][hapmap]
rs13161042	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1867447	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs34044107	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34434279	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59446142	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6882944	0.93[ASN][1000 genomes]
rs7706876	0.93[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.96[TSI][hapmap];0.89[YRI][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9329092	0.94[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases
2	nsv1030437	chr5:179235423-179649944	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
3	nsv537982	chr5:179235423-179649944	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
4	nsv948909	chr5:179249099-179772640	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
5	nsv830561	chr5:179365637-179537012	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases
6	nsv1033706	chr5:179402769-179806356	Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
7	nsv1024592	chr5:179443133-179510642	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1348523	NOP16	cis	parietal	SCAN
rs1348523	RUFY1	cis	cerebellum	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179472400-179496600	Weak transcription	Stomach Mucosa	stomach
2	chr5:179474000-179496200	Weak transcription	Primary B cells from cord blood	blood
3	chr5:179476000-179497800	Weak transcription	Lung	lung
4	chr5:179476400-179496800	Weak transcription	Right Ventricle	heart
5	chr5:179478000-179496800	Weak transcription	Right Atrium	heart
6	chr5:179479800-179496800	Weak transcription	Psoas Muscle	Psoas
7	chr5:179480600-179496400	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr5:179481200-179496600	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr5:179482600-179496600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr5:179484200-179496400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr5:179486800-179496800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr5:179488600-179496800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr5:179493800-179496200	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr5:179494000-179495600	Enhancers	Primary neutrophils fromperipheralblood	blood
15	chr5:179494000-179496000	Enhancers	H1 Cell Line	embryonic stem cell
16	chr5:179494000-179496000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr5:179494000-179496400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
18	chr5:179494000-179496600	Enhancers	Fetal Lung	lung
19	chr5:179494000-179497200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr5:179494200-179495600	Enhancers	K562	blood
21	chr5:179494200-179496400	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr5:179494200-179496800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr5:179494200-179496800	Enhancers	Liver	Liver
24	chr5:179494400-179495600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr5:179494600-179496400	Enhancers	Colon Smooth Muscle	Colon
26	chr5:179494600-179496600	Active TSS	Brain Inferior Temporal Lobe	brain
27	chr5:179494800-179495600	Enhancers	Stomach Smooth Muscle	stomach
28	chr5:179494800-179495800	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr5:179494800-179495800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
30	chr5:179494800-179495800	Active TSS	Brain Angular Gyrus	brain
31	chr5:179494800-179495800	Flanking Active TSS	Brain Hippocampus Middle	brain
32	chr5:179494800-179495800	Enhancers	NHEK	skin
33	chr5:179494800-179496600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr5:179494800-179497000	Flanking Active TSS	Brain Germinal Matrix	brain
35	chr5:179494800-179498400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr5:179495000-179495600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
37	chr5:179495000-179495600	Active TSS	Cortex derived primary cultured neurospheres	brain
38	chr5:179495000-179495600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr5:179495000-179495600	Enhancers	Adipose Nuclei	Adipose
40	chr5:179495000-179495800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
41	chr5:179495000-179495800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
42	chr5:179495000-179495800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
43	chr5:179495000-179495800	Flanking Active TSS	Primary hematopoietic stem cells	blood
44	chr5:179495000-179496000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
45	chr5:179495000-179496600	Enhancers	Fetal Kidney	kidney
46	chr5:179495000-179496800	Enhancers	A549	lung
47	chr5:179495000-179497800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
48	chr5:179495200-179495600	Enhancers	Primary hematopoietic stem cells short term culture	blood
49	chr5:179495200-179495600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr5:179495200-179495800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell

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