Variant report

Variant	rs2126283
Chromosome Location	chr4:91236962-91236963
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10015182	0.95[CEU][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes]
rs1023905	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs10516868	0.93[CEU][hapmap];0.88[EUR][1000 genomes]
rs11097246	0.88[EUR][1000 genomes]
rs11097247	0.86[CHB][hapmap]
rs11722282	0.84[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11723677	0.89[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11943083	0.88[EUR][1000 genomes]
rs12108481	0.88[EUR][1000 genomes]
rs12108488	0.84[CEU][hapmap];0.80[MEX][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs12639691	0.95[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12644644	0.90[EUR][1000 genomes]
rs12647511	0.90[EUR][1000 genomes]
rs13112637	0.88[EUR][1000 genomes]
rs13117351	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1350854	0.83[CEU][hapmap]
rs1461739	0.83[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1551794	1.00[CEU][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs17016698	0.89[TSI][hapmap]
rs17016807	0.88[EUR][1000 genomes]
rs2054350	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs2085915	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[JPT][hapmap]
rs2085916	1.00[CHB][hapmap]
rs34389744	0.92[EUR][1000 genomes]
rs34407211	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3775484	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6835475	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6842950	1.00[CHB][hapmap];0.96[CHD][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs733660	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs752367	0.87[EUR][1000 genomes]
rs7654964	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7668943	0.90[EUR][1000 genomes]
rs7688401	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9993515	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470053	chr4:90879613-91439573	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv931074	chr4:90970476-91753697	Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1007826	chr4:91049593-91438961	Enhancers Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv537177	chr4:91049593-91438961	Bivalent/Poised TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv999065	chr4:91049593-91520073	Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv879541	chr4:91156104-91253355	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv879542	chr4:91185206-91287204	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2126283	FAM190A	cis	cerebellum	SCAN
rs2126283	SMARCAD1	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:91222200-91244000	Weak transcription	Pancreas	Pancrea
2	chr4:91227200-91239000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr4:91228200-91244000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr4:91228400-91245000	Weak transcription	Primary B cells from peripheral blood	blood
5	chr4:91228600-91249600	Weak transcription	Primary hematopoietic stem cells	blood
6	chr4:91229800-91238800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr4:91229800-91246200	Weak transcription	Fetal Intestine Large	intestine
8	chr4:91230800-91239200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr4:91231800-91249600	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr4:91233400-91244000	Weak transcription	Fetal Intestine Small	intestine
11	chr4:91235000-91243400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr4:91235000-91244800	Weak transcription	Duodenum Mucosa	Duodenum
13	chr4:91236800-91237000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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