Variant report

Variant	rs792448
Chromosome Location	chr1:212558397-212558398
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:212554284..212555829-chr1:212557372..212559649,2	K562	blood:

Extended variants
information (count: 21 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs10019	0.86[YRI][hapmap]
rs1086893	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12035647	0.84[YRI][hapmap]
rs1539206	0.81[YRI][hapmap]
rs2252044	0.89[ASW][hapmap];0.81[LWK][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap]
rs3099112	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs351393	0.89[ASW][hapmap];0.88[LWK][hapmap];1.00[YRI][hapmap]
rs3767861	0.89[ASW][hapmap];0.87[MKK][hapmap];0.86[YRI][hapmap]
rs3767862	0.89[ASW][hapmap];0.87[MKK][hapmap];0.86[YRI][hapmap]
rs518793	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs612414	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs701905	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7415843	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs7519959	0.89[ASW][hapmap];0.87[MKK][hapmap];0.86[YRI][hapmap]
rs792447	0.91[LWK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009376	chr1:212292357-212680320	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
3	nsv997629	chr1:212404489-212658785	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv535286	chr1:212404489-212658785	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv1013110	chr1:212555764-212948092	Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
6	nsv535287	chr1:212555764-212948092	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs792448	NENF	cis	Esophagus Mucosa	GTEx
rs792448	TMEM206	cis	Esophagus Mucosa	GTEx
rs792448	LGTN	cis	cerebellum	SCAN
rs792448	TMEM206	cis	parietal	SCAN
rs792448	CD34	cis	cerebellum	SCAN
rs792448	TMEM206	cis	cerebellum	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212502600-212563400	Strong transcription	Primary monocytes fromperipheralblood	blood
2	chr1:212502600-212564600	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr1:212526800-212582800	Weak transcription	Fetal Brain Male	brain
4	chr1:212528400-212583000	Weak transcription	Fetal Kidney	kidney
5	chr1:212529400-212562400	Strong transcription	Dnd41	blood
6	chr1:212529800-212563200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr1:212532400-212560200	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr1:212534000-212570200	Weak transcription	HSMM	muscle
9	chr1:212534400-212570600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr1:212534600-212560000	Weak transcription	Colon Smooth Muscle	Colon
11	chr1:212535000-212561400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr1:212535200-212560200	Weak transcription	Hela-S3	cervix
13	chr1:212536200-212561600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr1:212538000-212571000	Weak transcription	NH-A	brain
15	chr1:212538200-212559600	Weak transcription	Right Atrium	heart
16	chr1:212540400-212575400	Weak transcription	HUVEC	blood vessel
17	chr1:212540600-212562600	Weak transcription	Osteobl	bone
18	chr1:212540600-212564000	Weak transcription	Stomach Mucosa	stomach
19	chr1:212542800-212561600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr1:212543600-212565200	Weak transcription	Fetal Lung	lung
21	chr1:212545000-212561000	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr1:212546800-212560200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr1:212546800-212560400	Strong transcription	Primary T helper cells PMA-I stimulated	--
24	chr1:212547000-212562600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr1:212547000-212563400	Strong transcription	Fetal Thymus	thymus
26	chr1:212547200-212561000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:212547400-212562400	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr1:212547400-212562400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr1:212548200-212560600	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr1:212548600-212563800	Strong transcription	Primary T cells from cord blood	blood
31	chr1:212548800-212558800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr1:212549400-212560600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr1:212549400-212561000	Strong transcription	Primary B cells from peripheral blood	blood
34	chr1:212549600-212560200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr1:212549800-212558600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr1:212550400-212561000	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr1:212550400-212562800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr1:212551400-212561800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr1:212551600-212560000	Weak transcription	Colonic Mucosa	Colon
40	chr1:212552000-212559600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr1:212552000-212562000	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr1:212553000-212562600	Strong transcription	GM12878-XiMat	blood
43	chr1:212553200-212558600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr1:212553200-212562000	Weak transcription	Liver	Liver
45	chr1:212553200-212569400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr1:212553200-212578400	Weak transcription	K562	blood
47	chr1:212553400-212560200	Weak transcription	Right Ventricle	heart
48	chr1:212553600-212558600	Weak transcription	HMEC	breast
49	chr1:212554600-212560600	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr1:212554600-212560600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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