Variant report

Variant	rs2089252
Chromosome Location	chr4:76830648-76830649
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10518141	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11930088	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13130621	1.00[TSI][hapmap]
rs2047984	1.00[EUR][1000 genomes]
rs2135232	0.82[YRI][hapmap]
rs4241574	1.00[TSI][hapmap]
rs4859410	1.00[TSI][hapmap]
rs4859564	1.00[TSI][hapmap]
rs60011229	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6532010	1.00[EUR][1000 genomes]
rs73825577	1.00[EUR][1000 genomes]
rs7664613	1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs7691712	1.00[TSI][hapmap]
rs7694386	1.00[TSI][hapmap]
rs9994323	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]

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	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
4	esv3467205	chr4:76825660-76831970	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region	1 gene(s)	inside rSNPs	diseases
5	esv3467206	chr4:76825660-76831970	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2089252	NAAA	cis	lymphoblastoid	seeQTL
rs2089252	RCHY1	cis	lymphoblastoid	seeQTL

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76821600-76831000	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr4:76823000-76836600	Weak transcription	Spleen	Spleen
3	chr4:76823600-76835000	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr4:76823800-76835000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr4:76824000-76835200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr4:76824800-76841000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr4:76827600-76841000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr4:76827800-76836600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr4:76829400-76835000	Weak transcription	Primary B cells from peripheral blood	blood
10	chr4:76829400-76836600	Weak transcription	Placenta	Placenta
11	chr4:76829400-76836600	Weak transcription	Ovary	ovary
12	chr4:76830000-76833000	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
13	chr4:76830000-76834200	Weak transcription	HSMMtube	muscle
14	chr4:76830000-76837000	Weak transcription	Rectal Smooth Muscle	rectum
15	chr4:76830200-76831000	Enhancers	Monocytes-CD14+_RO01746	blood
16	chr4:76830200-76835000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr4:76830200-76839600	Weak transcription	Primary B cells from cord blood	blood
18	chr4:76830400-76833800	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr4:76830400-76838200	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr4:76830400-76838600	Weak transcription	Fetal Muscle Leg	muscle
21	chr4:76830600-76831400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr4:76830600-76838200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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