Variant report

Variant	rs1876633
Chromosome Location	chr5:90235367-90235368
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:89703602..89706051-chr5:90235055..90237032,2	K562	blood:
2	chr5:90228479..90231902-chr5:90233871..90236526,4	K562	blood:
3	chr5:90233883..90235980-chr5:90676996..90679311,2	MCF-7	breast:
4	chr5:90229694..90231320-chr5:90235004..90237466,2	K562	blood:
5	chr5:90233758..90236433-chr5:90675781..90678446,3	K562	blood:
6	chr5:90233676..90235541-chr5:90674285..90677048,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000113369	Chromatin interaction
ENSG00000255647	Chromatin interaction
ENSG00000153140	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10078568	0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2063245	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap]
rs3105791	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3105792	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3114652	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3114654	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36131676	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4916696	0.94[ASN][1000 genomes]
rs4916697	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4916832	0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs6891672	0.81[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529544	chr5:89523963-90412409	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv517049	chr5:90003131-90262475	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1876633	MCTP1	cis	cerebellum	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:90225800-90236200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr5:90225800-90244000	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr5:90228400-90239200	Weak transcription	Aorta	Aorta
4	chr5:90229400-90235600	Weak transcription	Rectal Smooth Muscle	rectum
5	chr5:90229800-90235800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr5:90229800-90235800	Weak transcription	Fetal Stomach	stomach
7	chr5:90230400-90265200	Weak transcription	K562	blood
8	chr5:90230800-90235800	Weak transcription	HepG2	liver
9	chr5:90231600-90250800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr5:90234600-90236800	Enhancers	HUVEC	blood vessel
11	chr5:90234600-90237600	Enhancers	A549	lung
12	chr5:90234800-90237000	Enhancers	NHEK	skin
13	chr5:90234800-90237600	Enhancers	Pancreatic Islets	Pancreatic Islet
14	chr5:90234800-90237800	Enhancers	Colon Smooth Muscle	Colon
15	chr5:90235000-90235400	Enhancers	Brain Germinal Matrix	brain
16	chr5:90235000-90236000	Weak transcription	GM12878-XiMat	blood
17	chr5:90235000-90236800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr5:90235000-90236800	Enhancers	NH-A	brain
19	chr5:90235000-90237000	Enhancers	Muscle Satellite Cultured Cells	--
20	chr5:90235000-90237000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr5:90235000-90237400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr5:90235000-90238400	Enhancers	Fetal Kidney	kidney
23	chr5:90235200-90235400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr5:90235200-90235400	Enhancers	Fetal Brain Female	brain
25	chr5:90235200-90235600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr5:90235200-90235600	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr5:90235200-90236000	Weak transcription	Stomach Mucosa	stomach
28	chr5:90235200-90236800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr5:90235200-90236800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr5:90235200-90237600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr5:90235200-90237600	Enhancers	iPS-15b Cell Line	embryonic stem cell

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