Variant report

Variant	rs699829
Chromosome Location	chr1:76546051-76546052
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	chr1:76538798..76540470-chr1:76545089..76547752,3	K562	blood:

Variant related genes	Relation type
ENSG00000184005	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10493580	1.00[AFR][1000 genomes]
rs11162079	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1144343	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1144346	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1146663	0.98[ASN][1000 genomes]
rs12039427	0.85[AMR][1000 genomes]
rs1251576	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1251806	0.86[ASN][1000 genomes]
rs12568806	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1417407	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1763465	0.91[ASN][1000 genomes]
rs291075	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4146895	0.87[AMR][1000 genomes]
rs4146896	0.87[AMR][1000 genomes]
rs58483436	0.91[AMR][1000 genomes]
rs699830	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998499	chr1:76361784-76598712	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv870968	chr1:76490234-76552475	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv871862	chr1:76525783-76598209	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs699829	ACADM	cis	cerebellum	SCAN
rs699829	MSH4	cis	cerebellum	SCAN
rs699829	MSH4	cis	parietal	SCAN
rs699829	LRRIQ3	cis	cerebellum	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76541000-76546600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:76541200-76546600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr1:76541200-76551200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:76541600-76548000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr1:76541600-76550000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr1:76541800-76546200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:76541800-76547400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr1:76542000-76547400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:76542200-76546200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr1:76542200-76546400	Weak transcription	Colon Smooth Muscle	Colon
11	chr1:76542200-76546400	Weak transcription	Fetal Muscle Leg	muscle
12	chr1:76542200-76546600	Weak transcription	Fetal Brain Female	brain
13	chr1:76542200-76553200	Weak transcription	Fetal Intestine Large	intestine
14	chr1:76542400-76546200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr1:76542400-76546400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr1:76542400-76550000	Weak transcription	Primary B cells from peripheral blood	blood
17	chr1:76542800-76546400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr1:76542800-76546400	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr1:76542800-76547200	Weak transcription	Brain Angular Gyrus	brain
20	chr1:76542800-76572000	Weak transcription	Primary B cells from cord blood	blood
21	chr1:76543000-76546200	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr1:76543200-76546400	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr1:76544400-76546400	Weak transcription	Brain Cingulate Gyrus	brain
24	chr1:76545200-76546400	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr1:76545200-76548600	Enhancers	Brain Hippocampus Middle	brain
26	chr1:76545200-76548800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr1:76545400-76546200	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr1:76545400-76546400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr1:76545400-76551400	Enhancers	HUES6 Cell Line	embryonic stem cell
30	chr1:76545600-76546200	Weak transcription	Primary hematopoietic stem cells	blood
31	chr1:76545600-76546600	Enhancers	iPS-20b Cell Line	embryonic stem cell
32	chr1:76545600-76548000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:76545600-76548000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr1:76545600-76548600	Enhancers	Brain Substantia Nigra	brain
35	chr1:76545600-76549000	Weak transcription	Lung	lung
36	chr1:76545600-76552200	Weak transcription	Fetal Intestine Small	intestine
37	chr1:76545600-76558200	Weak transcription	Left Ventricle	heart
38	chr1:76545800-76546200	Weak transcription	Brain Anterior Caudate	brain
39	chr1:76545800-76546600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr1:76545800-76547400	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr1:76545800-76548000	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr1:76545800-76550600	Enhancers	Fetal Lung	lung
43	chr1:76546000-76546400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr1:76546000-76547000	Enhancers	Fetal Stomach	stomach
45	chr1:76546000-76548000	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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