Variant report

Variant	rs5749426
Chromosome Location	chr22:32795641-32795642
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:32793471..32796323-chr22:32803063..32805279,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100220	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11635	0.81[ASN][1000 genomes]
rs16990428	0.82[CHB][hapmap]
rs16990430	0.82[CHB][hapmap]
rs2049946	0.91[CHB][hapmap];0.83[JPT][hapmap];0.90[ASN][1000 genomes]
rs2049947	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2072815	0.86[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs2072816	0.83[CHB][hapmap]
rs2076041	0.80[ASN][1000 genomes]
rs2076042	0.88[YRI][hapmap];0.84[AFR][1000 genomes]
rs2076045	0.82[CHB][hapmap]
rs2076048	0.89[CHD][hapmap];0.83[JPT][hapmap]
rs2076049	0.83[JPT][hapmap]
rs2142720	0.85[CHB][hapmap]
rs2281034	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs2281035	0.91[CHB][hapmap];0.82[ASN][1000 genomes]
rs2281036	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2294312	0.96[ASN][1000 genomes]
rs2294313	0.91[CHB][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs2413113	0.86[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs4140572	0.91[CHB][hapmap]
rs5749414	0.83[CHB][hapmap]
rs5749416	0.87[CHB][hapmap]
rs5749421	1.00[CEU][hapmap];0.88[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5749427	0.82[ASN][1000 genomes]
rs5749428	0.91[CHB][hapmap];0.82[ASN][1000 genomes]
rs5749429	0.91[CHB][hapmap];0.82[ASN][1000 genomes]
rs5749432	0.89[CHD][hapmap];0.83[JPT][hapmap]
rs5754020	0.86[JPT][hapmap]
rs5754060	0.80[ASN][1000 genomes]
rs5754063	0.81[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5754065	0.91[CHB][hapmap];0.82[ASN][1000 genomes]
rs5754066	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59895149	0.81[ASN][1000 genomes]
rs5994562	0.91[CHB][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs5998440	0.82[JPT][hapmap]
rs5998471	0.95[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.97[ASN][1000 genomes]
rs5998475	0.91[CHB][hapmap];0.80[ASN][1000 genomes]
rs5998478	0.91[CHB][hapmap];0.93[CHD][hapmap];0.83[JPT][hapmap];0.90[ASN][1000 genomes]
rs60953467	0.84[ASN][1000 genomes]
rs713790	0.91[CHB][hapmap];0.80[ASN][1000 genomes]
rs715629	0.86[LWK][hapmap];0.88[YRI][hapmap]
rs7287452	0.91[CHB][hapmap];0.82[CHD][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs737779	0.95[CHB][hapmap];0.83[JPT][hapmap];0.97[ASN][1000 genomes]
rs742096	0.91[CHB][hapmap];0.82[ASN][1000 genomes]
rs9609537	0.88[YRI][hapmap]
rs9609538	0.83[YRI][hapmap]

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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs5749426	RFPL3S	Cis_1M	lymphoblastoid	RTeQTL
rs5749426	OSBP2	cis	cerebellum	SCAN
rs5749426	C22orf28	cis	cerebellum	SCAN
rs5749426	CCDC157	cis	parietal	SCAN

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	chr22:32781200-32798200	Strong transcription	Thymus	Thymus
4	chr22:32781200-32799200	Strong transcription	Duodenum Smooth Muscle	Duodenum
5	chr22:32781200-32801200	Strong transcription	Fetal Stomach	stomach
6	chr22:32781200-32802200	Strong transcription	Primary B cells from peripheral blood	blood
7	chr22:32781200-32803200	Strong transcription	Duodenum Mucosa	Duodenum
8	chr22:32781200-32804000	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr22:32781200-32804200	Strong transcription	Stomach Smooth Muscle	stomach
10	chr22:32781200-32804600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr22:32781200-32804600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr22:32781200-32804800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr22:32781200-32805000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr22:32781200-32805400	Strong transcription	Fetal Muscle Leg	muscle
15	chr22:32781200-32806600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr22:32781400-32798200	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr22:32781400-32798200	Strong transcription	Brain Anterior Caudate	brain
18	chr22:32781400-32798200	Strong transcription	NH-A	brain
19	chr22:32781400-32799200	Strong transcription	Lung	lung
20	chr22:32781400-32801200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr22:32781400-32802600	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr22:32781400-32802600	Strong transcription	GM12878-XiMat	blood
23	chr22:32781400-32802600	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr22:32781400-32803200	Strong transcription	Adipose Nuclei	Adipose
25	chr22:32781400-32803200	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr22:32781400-32803600	Strong transcription	Rectal Mucosa Donor 31	rectum
27	chr22:32781400-32803800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr22:32781400-32803800	Strong transcription	Liver	Liver
29	chr22:32781400-32804400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr22:32781400-32804600	Strong transcription	Fetal Thymus	thymus
31	chr22:32781400-32804600	Strong transcription	Skeletal Muscle Male	skeletal muscle
32	chr22:32781400-32804600	Strong transcription	Dnd41	blood
33	chr22:32781400-32804800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr22:32781400-32804800	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr22:32781400-32804800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr22:32781400-32804800	Strong transcription	Skeletal Muscle Female	skeletal muscle
37	chr22:32781400-32805000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr22:32781400-32805000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr22:32781400-32805000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr22:32781400-32805000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr22:32781400-32805000	Strong transcription	Fetal Intestine Large	intestine
42	chr22:32781400-32805000	Strong transcription	Fetal Lung	lung
43	chr22:32781400-32805000	Strong transcription	Fetal Muscle Trunk	muscle
44	chr22:32781400-32805000	Strong transcription	Left Ventricle	heart
45	chr22:32781400-32805000	Strong transcription	Osteobl	bone
46	chr22:32781400-32805200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
47	chr22:32781400-32805200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr22:32781400-32805600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr22:32781400-32806400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr22:32781400-32806600	Strong transcription	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links