Variant report

Variant	rs324420
Chromosome Location	chr1:46870761-46870762
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr1:46870721-46870784	K562	blood:	n/a	n/a
2	SPI1	chr1:46870575-46870817	K562	blood:	n/a	chr1:46870669-46870682 chr1:46870670-46870679 chr1:46870668-46870681
3	SPI1	chr1:46870439-46870872	HL-60	blood:	n/a	chr1:46870669-46870682 chr1:46870670-46870679 chr1:46870668-46870681

Variant related genes	Relation type
FAAH	TF binding region

Extended variants
information (count: 22 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10489770	0.82[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.93[MEX][hapmap]
rs12029329	0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1547180	0.86[ASW][hapmap]
rs1571138	0.93[ASW][hapmap];1.00[CEU][hapmap];0.87[CHD][hapmap];0.83[LWK][hapmap];0.81[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2145408	1.00[ASW][hapmap];0.80[CHB][hapmap];0.95[CHD][hapmap];0.93[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2295633	0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs324418	0.93[ASW][hapmap];0.85[CEU][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.96[TSI][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4660346	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4660928	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6429600	1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6670926	0.84[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6678149	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6689182	0.87[MEX][hapmap]
rs7555240	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005189	chr1:46335186-46949309	Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv534946	chr1:46335186-46949309	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	esv2761743	chr1:46339858-47026743	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
4	nsv829748	chr1:46724508-46876122	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	nsv546162	chr1:46807597-46870761	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1001455	chr1:46828004-47326539	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv534950	chr1:46828004-47326539	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
8	nsv1000562	chr1:46832451-47027044	Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs324420	SNORD55	cis	parietal	SCAN
rs324420	NSUN4	cis	lymphoblastoid	seeQTL
rs324420	MMACHC	cis	cerebellum	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46861000-46874400	Weak transcription	Primary T cells from cord blood	blood
2	chr1:46861200-46872200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr1:46861200-46879000	Weak transcription	Aorta	Aorta
4	chr1:46861200-46879400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr1:46861600-46880400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr1:46864000-46872400	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr1:46865400-46876000	Weak transcription	Primary hematopoietic stem cells	blood
8	chr1:46866200-46872000	Weak transcription	Primary B cells from peripheral blood	blood
9	chr1:46866400-46872600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr1:46867800-46871800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr1:46867800-46871800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr1:46867800-46872400	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr1:46867800-46872600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr1:46867800-46872600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr1:46867800-46872600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr1:46867800-46877000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr1:46868000-46870800	Weak transcription	Lung	lung
18	chr1:46868000-46871400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:46868000-46871600	Weak transcription	Right Ventricle	heart
20	chr1:46868000-46871800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr1:46868000-46871800	Weak transcription	Esophagus	oesophagus
22	chr1:46868000-46871800	Weak transcription	Placenta	Placenta
23	chr1:46868000-46871800	Weak transcription	Psoas Muscle	Psoas
24	chr1:46868000-46872000	Weak transcription	Colon Smooth Muscle	Colon
25	chr1:46868000-46876200	Weak transcription	Small Intestine	intestine
26	chr1:46868000-46884200	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr1:46868200-46871400	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr1:46868200-46871600	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr1:46868200-46871600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr1:46868200-46871600	Weak transcription	Adipose Nuclei	Adipose
31	chr1:46868200-46871600	Weak transcription	Fetal Brain Male	brain
32	chr1:46868200-46871600	Weak transcription	Fetal Muscle Trunk	muscle
33	chr1:46868200-46871600	Weak transcription	Ovary	ovary
34	chr1:46868200-46871600	Weak transcription	Spleen	Spleen
35	chr1:46868200-46871800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr1:46868200-46871800	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr1:46868200-46871800	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr1:46868200-46871800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr1:46868200-46871800	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr1:46868200-46871800	Weak transcription	Fetal Heart	heart
41	chr1:46868200-46871800	Weak transcription	Fetal Lung	lung
42	chr1:46868200-46871800	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr1:46868200-46871800	Weak transcription	Right Atrium	heart
44	chr1:46868200-46871800	Weak transcription	Hela-S3	cervix
45	chr1:46868200-46872000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr1:46868200-46872000	Weak transcription	Fetal Brain Female	brain
47	chr1:46868200-46872000	Weak transcription	Left Ventricle	heart
48	chr1:46868200-46872200	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr1:46868200-46873200	Weak transcription	Fetal Intestine Large	intestine
50	chr1:46868200-46873600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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