Variant report

Variant	rs7583634
Chromosome Location	chr2:48426035-48426036
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10186770	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10197197	1.00[ASN][1000 genomes]
rs1112259	1.00[ASW][hapmap];0.80[CEU][hapmap];0.83[CHB][hapmap];0.98[TSI][hapmap];0.85[EUR][1000 genomes]
rs11678411	0.98[ASN][1000 genomes]
rs11695011	0.86[EUR][1000 genomes]
rs11899562	0.91[EUR][1000 genomes]
rs12469811	0.92[CEU][hapmap];0.83[CHB][hapmap];0.97[EUR][1000 genomes]
rs12621844	0.89[EUR][1000 genomes]
rs12713006	0.83[CHB][hapmap]
rs13010470	0.83[CHB][hapmap]
rs1396826	1.00[ASW][hapmap];0.96[CEU][hapmap];0.92[CHB][hapmap];0.97[GIH][hapmap];0.88[LWK][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs1567397	0.83[CHB][hapmap];0.95[GIH][hapmap]
rs2175138	1.00[CEU][hapmap];0.92[CHB][hapmap];0.97[EUR][1000 genomes]
rs2348719	0.92[EUR][1000 genomes]
rs2348724	0.90[EUR][1000 genomes]
rs2882004	0.85[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs4953559	0.93[EUR][1000 genomes]
rs4953560	0.93[EUR][1000 genomes]
rs4953561	0.93[EUR][1000 genomes]
rs4953567	0.83[CHB][hapmap]
rs60068013	0.91[ASN][1000 genomes]
rs62137435	0.91[ASN][1000 genomes]
rs6545024	0.88[CEU][hapmap];0.83[CHB][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs67114103	0.97[ASN][1000 genomes]
rs6751603	0.80[CEU][hapmap];0.83[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6755968	0.92[CHB][hapmap]
rs7569620	0.80[ASN][1000 genomes]
rs7578930	0.97[ASN][1000 genomes]
rs7589085	1.00[ASN][1000 genomes]
rs876871	0.80[CEU][hapmap];0.83[CHB][hapmap];0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs883795	0.90[EUR][1000 genomes]
rs906857	0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009769	chr2:47972642-48509765	Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv535680	chr2:47972642-48509765	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv530831	chr2:48059709-48632317	Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv519831	chr2:48072855-48566031	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv1003766	chr2:48102244-48559654	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv581773	chr2:48277490-48443109	Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv1005241	chr2:48413134-48493182	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	esv2762552	chr2:48413146-48493182	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv457407	chr2:48414735-48493182	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv581774	chr2:48414735-48493182	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv1001850	chr2:48421389-48492090	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv535681	chr2:48421389-48492090	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7583634	FOXN2	cis	parietal	SCAN
rs7583634	FOXN2	cis	cerebellum	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48422000-48426400	Enhancers	Primary neutrophils fromperipheralblood	blood
2	chr2:48423200-48426800	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr2:48423400-48426600	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr2:48423400-48428200	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr2:48423600-48432600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr2:48423800-48426400	Weak transcription	Left Ventricle	heart
7	chr2:48423800-48435800	Weak transcription	Right Atrium	heart
8	chr2:48424000-48426200	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr2:48424000-48432400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:48424600-48426200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr2:48424600-48426200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr2:48424600-48426200	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr2:48424600-48426400	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr2:48424600-48426400	Weak transcription	GM12878-XiMat	blood
15	chr2:48424600-48428200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr2:48424600-48431400	Weak transcription	Brain Angular Gyrus	brain
17	chr2:48424600-48432600	Weak transcription	HSMMtube	muscle
18	chr2:48424600-48434000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr2:48424800-48434000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr2:48425000-48426200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr2:48425000-48426200	Weak transcription	Duodenum Mucosa	Duodenum
22	chr2:48425000-48429400	Weak transcription	Liver	Liver
23	chr2:48425200-48426200	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr2:48425200-48431800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr2:48425600-48426200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
26	chr2:48425600-48426600	Enhancers	HUES64 Cell Line	embryonic stem cell
27	chr2:48425800-48426200	Enhancers	Primary B cells from peripheral blood	blood
28	chr2:48426000-48426200	Enhancers	Right Ventricle	heart
29	chr2:48426000-48426200	Enhancers	Spleen	Spleen
30	chr2:48426000-48426400	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr2:48426000-48426600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr2:48426000-48426600	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr2:48426000-48426600	Enhancers	Brain Anterior Caudate	brain
34	chr2:48426000-48426600	Enhancers	Brain Cingulate Gyrus	brain
35	chr2:48426000-48426600	Enhancers	Brain Hippocampus Middle	brain
36	chr2:48426000-48426600	Enhancers	Brain Substantia Nigra	brain
37	chr2:48426000-48426600	Enhancers	Fetal Heart	heart
38	chr2:48426000-48426600	Enhancers	Fetal Muscle Leg	muscle
39	chr2:48426000-48426600	Bivalent Enhancer	HepG2	liver
40	chr2:48426000-48426800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr2:48426000-48426800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr2:48426000-48426800	Enhancers	iPS-18 Cell Line	embryonic stem cell
43	chr2:48426000-48426800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
44	chr2:48426000-48426800	Enhancers	Cortex derived primary cultured neurospheres	brain
45	chr2:48426000-48426800	Enhancers	Fetal Muscle Trunk	muscle
46	chr2:48426000-48426800	Enhancers	K562	blood
47	chr2:48426000-48427000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr2:48426000-48427400	Enhancers	HUES48 Cell Line	embryonic stem cell
49	chr2:48426000-48428000	Enhancers	iPS-20b Cell Line	embryonic stem cell

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