Variant report

Variant	rs1852731
Chromosome Location	chr5:90392621-90392622
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:90389673..90399904-chr5:90673387..90683638,16	K562	blood:

Variant related genes	Relation type
ENSG00000113369	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs12109264	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16869403	0.81[CEU][hapmap];0.90[CHB][hapmap];0.80[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16869404	0.90[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16869414	0.90[CEU][hapmap];0.90[CHB][hapmap];0.81[CHD][hapmap];0.83[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16869425	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1876635	0.81[CEU][hapmap];0.82[CHB][hapmap];0.80[JPT][hapmap];0.88[MEX][hapmap]
rs1986718	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2950849	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2950850	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2950851	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2950852	0.91[CEU][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2950853	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2950854	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2950855	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2973444	0.90[CEU][hapmap]
rs2973445	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2973447	1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2973448	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2973449	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2973450	1.00[CEU][hapmap];0.84[CHD][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2973453	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2973454	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2973455	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2973456	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3112484	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3952745	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56137437	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56377639	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs58524182	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59654682	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59661306	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61392689	0.95[ASN][1000 genomes]
rs66482530	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs66608099	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6874106	0.90[CEU][hapmap];0.90[CHB][hapmap];0.81[CHD][hapmap];0.83[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73187190	0.95[ASN][1000 genomes]
rs73189008	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv1024813	chr5:90321535-90870739	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
3	nsv537806	chr5:90321535-90870739	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1852731	MCTP1	cis	cerebellum	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:90370600-90397600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:90385800-90397400	Weak transcription	Fetal Lung	lung
3	chr5:90386800-90400800	Weak transcription	K562	blood
4	chr5:90387800-90397600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr5:90390800-90394400	Weak transcription	HSMM	muscle
6	chr5:90391000-90394400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr5:90391000-90397000	Weak transcription	A549	lung
8	chr5:90391200-90392800	Enhancers	Brain Anterior Caudate	brain
9	chr5:90391200-90393200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr5:90391200-90395000	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr5:90391400-90393600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
12	chr5:90391600-90392800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr5:90391600-90392800	Enhancers	Brain Germinal Matrix	brain
14	chr5:90391800-90392800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr5:90391800-90392800	Enhancers	Rectal Smooth Muscle	rectum
16	chr5:90391800-90393000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr5:90391800-90397600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr5:90392000-90393000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr5:90392000-90393000	Enhancers	Colon Smooth Muscle	Colon
20	chr5:90392000-90393000	Enhancers	Fetal Kidney	kidney
21	chr5:90392000-90397400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr5:90392000-90397400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr5:90392000-90400800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr5:90392200-90392800	Enhancers	Fetal Heart	heart
25	chr5:90392200-90393000	Enhancers	Fetal Brain Male	brain
26	chr5:90392200-90400800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr5:90392400-90393000	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr5:90392400-90393000	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr5:90392400-90393000	Enhancers	iPS-20b Cell Line	embryonic stem cell
30	chr5:90392400-90393200	Enhancers	iPS-18 Cell Line	embryonic stem cell
31	chr5:90392400-90393200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr5:90392400-90393200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr5:90392400-90393600	Enhancers	H9 Cell Line	embryonic stem cell
34	chr5:90392600-90392800	Enhancers	H1 Cell Line	embryonic stem cell
35	chr5:90392600-90392800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr5:90392600-90392800	Enhancers	Adipose Nuclei	Adipose
37	chr5:90392600-90393000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr5:90392600-90394400	Enhancers	HUES64 Cell Line	embryonic stem cell
39	chr5:90392600-90395200	Enhancers	HUES48 Cell Line	embryonic stem cell
40	chr5:90392600-90399200	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr5:90392600-90400800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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