Variant report

Variant	rs4977749
Chromosome Location	chr9:21927327-21927328
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10811638	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10965183	0.94[CEU][hapmap];0.89[EUR][1000 genomes]
rs10965186	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2188125	0.89[CEU][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2518712	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2518713	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2518714	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2518715	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2811715	0.89[CEU][hapmap];0.95[CHD][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4977570	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4977746	1.00[CEU][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap];0.96[TSI][hapmap];0.93[EUR][1000 genomes]
rs4977747	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4977748	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6475597	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7852128	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7852234	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7864029	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7869004	1.00[CEU][hapmap];0.93[CHD][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.90[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	nsv529609	chr9:21708371-22537069	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv8426	chr9:21763810-22176200	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv892745	chr9:21857244-22006273	Bivalent Enhancer Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4977749	MTAP	cis	multi-tissue	Pritchard

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21905400-21931000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr9:21911000-21931200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr9:21911000-21935800	Weak transcription	HSMM	muscle
4	chr9:21916600-21930800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr9:21919800-21931000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr9:21919800-21931000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr9:21919800-21932800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr9:21920000-21931200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr9:21920200-21930400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr9:21920200-21931000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr9:21920400-21928400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr9:21920400-21931400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr9:21920400-21931600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr9:21920600-21935000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr9:21920600-21942600	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr9:21920800-21932000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr9:21921200-21931000	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr9:21921200-21934000	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr9:21921200-21935600	Weak transcription	Primary T cells from cord blood	blood
20	chr9:21922200-21932400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr9:21922200-21933000	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr9:21922800-21931000	Weak transcription	Aorta	Aorta
23	chr9:21923200-21930000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr9:21923600-21931000	Weak transcription	Fetal Stomach	stomach
25	chr9:21923800-21934000	Weak transcription	Thymus	Thymus
26	chr9:21923800-21934800	Weak transcription	Dnd41	blood
27	chr9:21924000-21934600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr9:21924800-21933000	Weak transcription	Lung	lung
29	chr9:21926200-21931200	Weak transcription	NHEK	skin
30	chr9:21927000-21933400	Weak transcription	HSMMtube	muscle

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