Variant report

Variant	rs9595937
Chromosome Location	chr13:49176935-49176936
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12855185	0.84[EUR][1000 genomes]
rs12859099	0.85[EUR][1000 genomes]
rs12876717	0.82[EUR][1000 genomes]
rs12877288	0.83[EUR][1000 genomes]
rs1808060	0.82[EUR][1000 genomes]
rs1887152	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1887154	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1951775	0.89[ASW][hapmap];0.81[CEU][hapmap];0.83[TSI][hapmap]
rs2407093	0.92[AFR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4497565	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7139578	0.90[ASW][hapmap];0.82[CEU][hapmap];0.84[MKK][hapmap];0.86[TSI][hapmap]
rs7325719	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7332322	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7336379	0.92[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs9316395	0.90[ASW][hapmap];0.82[CEU][hapmap];0.86[TSI][hapmap]
rs9316399	0.82[CEU][hapmap]
rs9316407	0.84[EUR][1000 genomes]
rs943278	0.82[CEU][hapmap]
rs943280	0.83[EUR][1000 genomes]
rs9526479	0.82[YRI][hapmap]
rs9535032	0.90[ASW][hapmap];0.82[CEU][hapmap];0.83[TSI][hapmap]
rs9535049	0.83[EUR][1000 genomes]
rs9535059	0.90[AFR][1000 genomes]
rs9562828	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9568051	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568059	0.90[AFR][1000 genomes]
rs9568069	0.90[AFR][1000 genomes]
rs964413	0.90[AFR][1000 genomes]
rs990814	0.89[ASW][hapmap];0.82[CEU][hapmap];0.86[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041275	chr13:49045566-49242357	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv541769	chr13:49045566-49242357	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv832604	chr13:49061081-49281807	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv1049117	chr13:49089476-49928945	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
5	nsv832605	chr13:49171305-49344970	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9595937	ITM2B	Cis_1M	lymphoblastoid	RTeQTL
rs9595937	LPAR6	cis	parietal	SCAN
rs9595937	ATAD2	trans	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49169800-49177800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr13:49174200-49177400	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr13:49174400-49177000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr13:49174600-49177000	Enhancers	Placenta Amnion	Placenta Amnion
5	chr13:49174600-49178000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr13:49174800-49177000	Enhancers	Primary hematopoietic stem cells	blood
7	chr13:49174800-49177200	Enhancers	Placenta	Placenta
8	chr13:49174800-49177400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr13:49175400-49177000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr13:49175400-49177000	Enhancers	Hela-S3	cervix
11	chr13:49175800-49177600	Enhancers	Dnd41	blood
12	chr13:49176400-49177200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr13:49176600-49177000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr13:49176600-49177400	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr13:49176600-49177600	Enhancers	H1 Cell Line	embryonic stem cell
16	chr13:49176800-49177000	Enhancers	Fetal Muscle Leg	muscle
17	chr13:49176800-49177200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr13:49176800-49177600	Weak transcription	NH-A	brain

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