Variant report

Variant	rs4256246
Chromosome Location	chr4:76945522-76945523
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs12651516	0.84[AFR][1000 genomes]
rs17001364	0.83[CHB][hapmap]
rs17001390	0.82[CHB][hapmap]
rs17506007	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.96[TSI][hapmap];0.90[ASN][1000 genomes]
rs4129780	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.91[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41349449	0.86[CHB][hapmap];0.91[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap]
rs41411447	0.86[CHB][hapmap];0.91[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap]
rs4308383	0.82[CHB][hapmap];1.00[YRI][hapmap]
rs58591414	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs60630277	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs61300528	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs6817952	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6825243	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7675618	0.86[CHB][hapmap]
rs867562	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs884002	0.92[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.89[AMR][1000 genomes];0.95[ASN][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	esv3353539	chr4:76530136-76993859	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv529613	chr4:76654941-77081576	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv1004627	chr4:76793910-76999584	Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4256246	NUP54	cis	Thyroid	GTEx
rs4256246	NUP54	cis	Nerve Tibial	GTEx
rs4256246	GDEP	cis	cerebellum	SCAN
rs4256246	CXCL11	cis	multi-tissue	Pritchard
rs4256246	NUP54	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76944200-76945800	Enhancers	Primary B cells from peripheral blood	blood
2	chr4:76944400-76945600	Enhancers	Primary hematopoietic stem cells short term culture	blood
3	chr4:76944400-76946200	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr4:76944600-76945800	Enhancers	Primary T helper cells fromperipheralblood	blood
5	chr4:76944600-76946000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr4:76944600-76946000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr4:76944800-76945800	Enhancers	Primary T helper cells PMA-I stimulated	--
8	chr4:76944800-76949200	Weak transcription	Fetal Lung	lung
9	chr4:76944800-76949600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr4:76945000-76945600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr4:76945000-76949200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr4:76945200-76945800	Enhancers	Monocytes-CD14+_RO01746	blood
13	chr4:76945200-76949600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr4:76945400-76945600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
15	chr4:76945400-76945600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr4:76945400-76946400	Enhancers	Primary hematopoietic stem cells	blood
17	chr4:76945400-76949200	Weak transcription	Adipose Nuclei	Adipose
18	chr4:76945400-76949200	Weak transcription	Liver	Liver
19	chr4:76945400-76949600	Weak transcription	Primary T helper memory cells from peripheral blood 1	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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