Variant report

Variant	rs11727844
Chromosome Location	chr4:79554063-79554064
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1042515	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11728517	0.82[ASN][1000 genomes]
rs11729862	0.81[JPT][hapmap]
rs11733032	0.88[YRI][hapmap]
rs11736376	0.90[YRI][hapmap]
rs12640075	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12641789	0.84[AMR][1000 genomes]
rs17003396	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35628566	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4382063	1.00[CEU][hapmap];0.89[CHB][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes]
rs56023152	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57415147	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57896096	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59133103	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5950	0.88[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6533842	0.89[YRI][hapmap]
rs67280698	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6817792	0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6819559	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6836185	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6837823	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72607862	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72607863	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72607864	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72607865	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72607866	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7661370	0.89[CHB][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs7668240	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7671564	0.90[YRI][hapmap]
rs7686273	0.80[CHB][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009633	chr4:78887573-79652236	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11727844	RP11-792D21.2	cis	Whole Blood	GTEx

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79542200-79555600	Enhancers	Fetal Intestine Small	intestine
2	chr4:79542600-79555600	Enhancers	Fetal Intestine Large	intestine
3	chr4:79548200-79555000	Weak transcription	Osteobl	bone
4	chr4:79548800-79557400	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr4:79549600-79560000	Weak transcription	HMEC	breast
6	chr4:79549800-79554200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr4:79550200-79556600	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr4:79550400-79555000	Weak transcription	NHDF-Ad	bronchial
9	chr4:79550400-79564200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr4:79551200-79554200	Weak transcription	Brain Hippocampus Middle	brain
11	chr4:79551200-79554400	Weak transcription	Brain Substantia Nigra	brain
12	chr4:79551400-79555200	Weak transcription	Right Atrium	heart
13	chr4:79551400-79558400	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr4:79551400-79578200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr4:79551600-79555000	Weak transcription	Adipose Nuclei	Adipose
16	chr4:79551600-79555600	Enhancers	Primary B cells from peripheral blood	blood
17	chr4:79552000-79554600	Enhancers	Primary B cells from cord blood	blood
18	chr4:79552600-79554600	Weak transcription	GM12878-XiMat	blood
19	chr4:79552800-79554800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr4:79553000-79561600	Weak transcription	Placenta	Placenta
21	chr4:79553200-79555200	Weak transcription	K562	blood
22	chr4:79553200-79559200	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr4:79553200-79559200	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr4:79553200-79563000	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr4:79553600-79554200	Enhancers	Left Ventricle	heart
26	chr4:79553800-79555200	Enhancers	Brain Anterior Caudate	brain
27	chr4:79553800-79555800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr4:79554000-79554200	Weak transcription	Brain Cingulate Gyrus	brain
29	chr4:79554000-79555400	Weak transcription	Pancreas	Pancrea
30	chr4:79554000-79558600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr4:79554000-79561600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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