Variant report

Variant	rs7296020
Chromosome Location	chr12:63309327-63309328
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:63300143..63303851-chr12:63306898..63309858,4	MCF-7	breast:
2	chr12:63303143..63306102-chr12:63308178..63311320,4	K562	blood:
3	chr12:63275413..63276960-chr12:63307773..63310580,2	K562	blood:
4	chr12:63292677..63295227-chr12:63307980..63310635,2	MCF-7	breast:
5	chr12:63307556..63310416-chr12:63316957..63319836,2	MCF-7	breast:
6	chr12:63307451..63310079-chr12:63319442..63322699,3	MCF-7	breast:

Extended variants
information (count: 12 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1020452	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10877927	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10877928	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11174717	0.88[JPT][hapmap]
rs3911805	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7962438	0.94[CEU][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7962536	0.94[CEU][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7967481	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

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	esv3415227	chr12:63228121-63591615	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv899161	chr12:63275017-63311148	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv899162	chr12:63279750-63334242	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
4	nsv899163	chr12:63288343-63325988	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7296020	MON2	cis	parietal	SCAN
rs7296020	NXPH4	cis	parietal	SCAN
rs7296020	TSPAN31	cis	cerebellum	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:63287800-63316400	Weak transcription	Fetal Intestine Small	intestine
2	chr12:63292800-63311600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr12:63297400-63309600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr12:63301200-63313400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr12:63301800-63313600	Weak transcription	Aorta	Aorta
6	chr12:63303400-63313000	Weak transcription	Ovary	ovary
7	chr12:63304800-63310200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr12:63305000-63313400	Weak transcription	Stomach Mucosa	stomach
9	chr12:63305000-63316800	Weak transcription	Fetal Intestine Large	intestine
10	chr12:63306600-63309800	Enhancers	H1 Cell Line	embryonic stem cell
11	chr12:63306600-63310200	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr12:63306600-63313400	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr12:63306800-63310000	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr12:63306800-63314000	Enhancers	Brain Angular Gyrus	brain
15	chr12:63307000-63309600	Enhancers	H9 Cell Line	embryonic stem cell
16	chr12:63307000-63310200	Strong transcription	HepG2	liver
17	chr12:63307000-63313800	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr12:63307000-63314000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr12:63307200-63309400	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr12:63307200-63309600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr12:63307200-63309800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr12:63307200-63311000	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr12:63307200-63314000	Enhancers	Brain Anterior Caudate	brain
24	chr12:63307400-63310800	Weak transcription	Fetal Kidney	kidney
25	chr12:63307800-63314400	Enhancers	Brain Hippocampus Middle	brain
26	chr12:63308000-63309400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
27	chr12:63308000-63313600	Enhancers	HUES64 Cell Line	embryonic stem cell
28	chr12:63308200-63315600	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr12:63308400-63309600	Enhancers	K562	blood
30	chr12:63308400-63313600	Enhancers	HUES48 Cell Line	embryonic stem cell
31	chr12:63308600-63309400	Enhancers	Monocytes-CD14+_RO01746	blood
32	chr12:63308600-63309800	Enhancers	iPS-20b Cell Line	embryonic stem cell
33	chr12:63308600-63310600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr12:63308600-63313600	Weak transcription	Primary hematopoietic stem cells	blood
35	chr12:63308600-63315800	Enhancers	Brain Substantia Nigra	brain
36	chr12:63308800-63311400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr12:63308800-63311800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr12:63308800-63313400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr12:63309000-63309400	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr12:63309000-63309600	Enhancers	Pancreas	Pancrea
41	chr12:63309000-63310600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr12:63309000-63311200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
43	chr12:63309200-63309400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr12:63309200-63309400	Flanking Active TSS	Brain Cingulate Gyrus	brain
45	chr12:63309200-63309600	Enhancers	Primary neutrophils fromperipheralblood	blood
46	chr12:63309200-63309600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr12:63309200-63309600	Enhancers	Left Ventricle	heart

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