Variant report

Variant	rs5749428
Chromosome Location	chr22:32799696-32799697
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:32799040..32801352-chr22:32805906..32808230,2	K562	blood:

Variant related genes	Relation type
ENSG00000100220	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs11089564	0.86[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs11635	0.99[ASN][1000 genomes]
rs11912349	0.90[ASN][1000 genomes]
rs12160986	0.80[CHB][hapmap];0.86[JPT][hapmap]
rs12628702	0.92[ASN][1000 genomes]
rs1543320	0.81[CHB][hapmap]
rs16987625	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs16990262	0.86[JPT][hapmap]
rs16990428	0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.94[ASN][1000 genomes]
rs16990430	0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.94[ASN][1000 genomes]
rs2014356	0.87[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.92[ASN][1000 genomes]
rs2049946	0.84[CHB][hapmap]
rs2072815	0.87[CHB][hapmap]
rs2072816	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2076041	0.99[ASN][1000 genomes]
rs2076045	0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.94[ASN][1000 genomes]
rs2281034	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2281035	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs2281036	0.87[CHB][hapmap]
rs2294311	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2294312	0.83[ASN][1000 genomes]
rs2294313	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2294314	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2413113	0.86[CHB][hapmap]
rs2899185	0.80[CHB][hapmap];0.86[JPT][hapmap]
rs4140572	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs5749412	0.81[JPT][hapmap]
rs5749413	0.86[JPT][hapmap]
rs5749414	0.92[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs5749416	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5749421	0.80[ASN][1000 genomes]
rs5749426	0.91[CHB][hapmap];0.82[ASN][1000 genomes]
rs5749427	1.00[ASN][1000 genomes]
rs5749429	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs5749433	0.92[ASN][1000 genomes]
rs5749436	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs5754003	0.80[CHB][hapmap];0.82[JPT][hapmap]
rs5754008	0.80[CHB][hapmap];0.86[JPT][hapmap]
rs5754009	0.86[JPT][hapmap]
rs5754010	0.80[CHB][hapmap];0.86[JPT][hapmap]
rs5754018	0.86[JPT][hapmap]
rs5754027	0.81[JPT][hapmap]
rs5754029	0.85[JPT][hapmap]
rs5754030	0.82[JPT][hapmap]
rs5754035	0.86[JPT][hapmap]
rs5754036	0.81[JPT][hapmap]
rs5754037	0.81[JPT][hapmap]
rs5754039	0.80[CHB][hapmap];0.86[JPT][hapmap]
rs5754040	0.82[JPT][hapmap]
rs5754042	0.80[CHB][hapmap];0.86[JPT][hapmap]
rs5754044	0.82[JPT][hapmap]
rs5754045	0.86[JPT][hapmap]
rs5754050	0.85[JPT][hapmap]
rs5754063	0.91[CHB][hapmap];0.80[ASN][1000 genomes]
rs5754065	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs5754066	0.92[CHB][hapmap];0.80[ASN][1000 genomes]
rs59895149	0.99[ASN][1000 genomes]
rs5994562	0.84[CHB][hapmap]
rs5998451	0.81[JPT][hapmap]
rs5998457	0.85[JPT][hapmap]
rs5998459	0.86[JPT][hapmap]
rs5998463	0.82[JPT][hapmap]
rs5998471	0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs5998475	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5998478	0.83[CHB][hapmap]
rs713790	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs72137940	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7287452	0.82[CHB][hapmap]
rs737779	0.96[CHB][hapmap];0.84[ASN][1000 genomes]
rs738267	0.81[JPT][hapmap]
rs742096	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv459874	chr22:32574274-32866934	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv588895	chr22:32574274-32866934	Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
3	nsv1064737	chr22:32603912-32829725	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
4	nsv1066118	chr22:32779078-32815334	Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs5749428	RFPL3S	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:32780800-32806400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr22:32780800-32806400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr22:32781200-32801200	Strong transcription	Fetal Stomach	stomach
4	chr22:32781200-32802200	Strong transcription	Primary B cells from peripheral blood	blood
5	chr22:32781200-32803200	Strong transcription	Duodenum Mucosa	Duodenum
6	chr22:32781200-32804000	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr22:32781200-32804200	Strong transcription	Stomach Smooth Muscle	stomach
8	chr22:32781200-32804600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr22:32781200-32804600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr22:32781200-32804800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr22:32781200-32805000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr22:32781200-32805400	Strong transcription	Fetal Muscle Leg	muscle
13	chr22:32781200-32806600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr22:32781400-32801200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr22:32781400-32802600	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr22:32781400-32802600	Strong transcription	GM12878-XiMat	blood
17	chr22:32781400-32802600	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr22:32781400-32803200	Strong transcription	Adipose Nuclei	Adipose
19	chr22:32781400-32803200	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr22:32781400-32803600	Strong transcription	Rectal Mucosa Donor 31	rectum
21	chr22:32781400-32803800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr22:32781400-32803800	Strong transcription	Liver	Liver
23	chr22:32781400-32804400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr22:32781400-32804600	Strong transcription	Fetal Thymus	thymus
25	chr22:32781400-32804600	Strong transcription	Skeletal Muscle Male	skeletal muscle
26	chr22:32781400-32804600	Strong transcription	Dnd41	blood
27	chr22:32781400-32804800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr22:32781400-32804800	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr22:32781400-32804800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr22:32781400-32804800	Strong transcription	Skeletal Muscle Female	skeletal muscle
31	chr22:32781400-32805000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr22:32781400-32805000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr22:32781400-32805000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr22:32781400-32805000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr22:32781400-32805000	Strong transcription	Fetal Intestine Large	intestine
36	chr22:32781400-32805000	Strong transcription	Fetal Lung	lung
37	chr22:32781400-32805000	Strong transcription	Fetal Muscle Trunk	muscle
38	chr22:32781400-32805000	Strong transcription	Left Ventricle	heart
39	chr22:32781400-32805000	Strong transcription	Osteobl	bone
40	chr22:32781400-32805200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr22:32781400-32805200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr22:32781400-32805600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr22:32781400-32806400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr22:32781400-32806600	Strong transcription	Placenta	Placenta
45	chr22:32781600-32804800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr22:32781600-32804800	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr22:32781600-32805000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr22:32781600-32805000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr22:32781600-32805400	Strong transcription	HUES64 Cell Line	embryonic stem cell
50	chr22:32781600-32806000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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