Variant report

Variant	rs12869642
Chromosome Location	chr13:51642548-51642549
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:51636070..51637847-chr13:51641416..51643792,2	K562	blood:
2	chr13:51633296..51638107-chr13:51641307..51645101,5	MCF-7	breast:
3	chr13:51632808..51634425-chr13:51641249..51643294,2	K562	blood:
4	chr13:51544110..51545950-chr13:51641591..51643167,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000123201	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs12870315	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12870383	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1328358	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4605050	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4942946	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6561609	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6561610	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7325888	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7337587	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7338712	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7990559	0.82[AMR][1000 genomes]
rs9535567	0.85[ASN][1000 genomes]
rs9563016	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9596435	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832610	chr13:51636661-51822106	Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12869642	GUCY1B2	cis	Esophagus Mucosa	GTEx
rs12869642	GUCY1B2	cis	Skin Sun Exposed Lower leg	GTEx
rs12869642	GUCY1B2	cis	Nerve Tibial	GTEx
rs12869642	GUCY1B2	cis	lung	GTEx

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:51633400-51657800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr13:51638000-51644600	Enhancers	Fetal Brain Male	brain
3	chr13:51639200-51644000	Weak transcription	Fetal Kidney	kidney
4	chr13:51640000-51644200	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr13:51640200-51644600	Enhancers	Fetal Heart	heart
6	chr13:51641000-51642800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr13:51641000-51643000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr13:51641000-51643800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr13:51641000-51644000	Weak transcription	HSMM	muscle
10	chr13:51641200-51644000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr13:51641200-51644200	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr13:51641400-51643200	Weak transcription	Adipose Nuclei	Adipose
13	chr13:51641400-51643600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr13:51641400-51644000	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr13:51641400-51644000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr13:51641400-51644000	Weak transcription	Brain Cingulate Gyrus	brain
17	chr13:51641400-51644000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr13:51641400-51644000	Weak transcription	Fetal Thymus	thymus
19	chr13:51641400-51644000	Enhancers	Dnd41	blood
20	chr13:51641600-51643000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr13:51641600-51643600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr13:51641600-51643800	Weak transcription	Primary hematopoietic stem cells	blood
23	chr13:51641600-51644000	Weak transcription	Brain Angular Gyrus	brain
24	chr13:51641600-51644000	Weak transcription	Fetal Muscle Leg	muscle
25	chr13:51641800-51643800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr13:51641800-51643800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr13:51641800-51643800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr13:51641800-51644000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr13:51641800-51644000	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr13:51641800-51644000	Weak transcription	NH-A	brain
31	chr13:51641800-51645600	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr13:51642000-51644600	Enhancers	Fetal Lung	lung
33	chr13:51642200-51642600	Flanking Active TSS	Brain Germinal Matrix	brain
34	chr13:51642200-51642600	Flanking Active TSS	Fetal Brain Female	brain
35	chr13:51642400-51642600	Bivalent Enhancer	HepG2	liver

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