Variant report

Variant	rs11053548
Chromosome Location	chr12:10170727-10170728
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10505745	0.86[ASN][1000 genomes]
rs11053536	0.85[CHB][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs11053538	0.87[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs11053549	0.87[ASN][1000 genomes]
rs11053550	0.87[ASN][1000 genomes]
rs11053554	0.86[ASN][1000 genomes]
rs11053555	0.86[ASN][1000 genomes]
rs11053556	0.86[ASN][1000 genomes]
rs12228507	0.87[ASN][1000 genomes]
rs12230249	0.86[ASN][1000 genomes]
rs12819440	0.87[ASN][1000 genomes]
rs2273987	0.87[CHB][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs3818343	0.87[CHB][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs3903805	0.81[ASN][1000 genomes]
rs56906784	0.87[ASN][1000 genomes]
rs652944	0.93[JPT][hapmap]
rs673173	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs676397	0.81[CHB][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	nsv898755	chr12:10069302-10186284	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv1043125	chr12:10121288-10177037	Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1042106	chr12:10121288-10177636	Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1040610	chr12:10121288-10179374	Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv898756	chr12:10142538-10174314	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Systolic blood pressure in sickle cell anemia	24058526	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11053548	SCARNA10	cis	cerebellum	SCAN
rs11053548	VWF	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:10167600-10170800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr12:10168800-10171600	Enhancers	HUVEC	blood vessel
3	chr12:10169600-10171600	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr12:10169600-10171800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr12:10169800-10172200	Enhancers	Primary hematopoietic stem cells	blood
6	chr12:10170000-10171000	Enhancers	Stomach Smooth Muscle	stomach
7	chr12:10170000-10171600	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr12:10170000-10172000	Enhancers	Fetal Stomach	stomach
9	chr12:10170200-10171200	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr12:10170200-10171400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr12:10170200-10180200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr12:10170400-10171600	Genic enhancers	Monocytes-CD14+_RO01746	blood
13	chr12:10170600-10171200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr12:10170600-10179600	Weak transcription	Primary neutrophils fromperipheralblood	blood

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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