Variant report

Variant	rs12142240
Chromosome Location	chr1:46747301-46747302
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:38)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:38 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:46746329-46747312	GM12891	blood:	n/a	n/a
2	POLR2A	chr1:46740032-46753254	HepG2	liver:	n/a	n/a
3	POLR2A	chr1:46736091-46756111	GM12892	blood:	n/a	n/a
4	POLR2A	chr1:46746299-46747301	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr1:46747257-46747474	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr1:46746862-46747365	A549	lung:	n/a	n/a
7	POLR2A	chr1:46745971-46747336	MCF-7	breast:	n/a	n/a
8	POLR2A	chr1:46742834-46747432	K562	blood:	n/a	n/a
9	POLR2A	chr1:46742643-46747471	K562	blood:	n/a	n/a
10	POLR2A	chr1:46739760-46752764	SK-N-MC	brain:	n/a	n/a
11	POLR2A	chr1:46743079-46747473	K562	blood:	n/a	n/a
12	POLR2A	chr1:46747264-46747372	GM12878	blood:	n/a	n/a
13	POLR2A	chr1:46743104-46749361	K562	blood:	n/a	n/a
14	MTA3	chr1:46745834-46747436	GM12878	blood:	n/a	n/a
15	PML	chr1:46746189-46747426	GM12878	blood:	n/a	n/a
16	POLR2A	chr1:46738421-46756429	K562	blood:	n/a	n/a
17	POLR2A	chr1:46744136-46747404	U87	brain:	n/a	n/a
18	POLR2A	chr1:46743419-46747316	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr1:46744140-46747444	GM12878	blood:	n/a	n/a
20	POLR2A	chr1:46744142-46747516	U87	brain:	n/a	n/a
21	POLR2A	chr1:46747157-46747312	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr1:46743197-46747322	K562	blood:	n/a	n/a
23	POLR2A	chr1:46738173-46747449	GM12878	blood:	n/a	n/a
24	POLR2A	chr1:46744050-46748777	K562	blood:	n/a	n/a
25	POLR2A	chr1:46744115-46747528	GM12878	blood:	n/a	n/a
26	POLR2A	chr1:46743393-46747610	PFSK-1	brain:	n/a	n/a
27	POLR2A	chr1:46747173-46747482	GM12878	blood:	n/a	n/a
28	POLR2A	chr1:46746306-46747500	GM12892	blood:	n/a	n/a
29	POLR2A	chr1:46741735-46749542	PFSK-1	brain:	n/a	n/a
30	POLR2A	chr1:46742615-46747480	HepG2	liver:	n/a	n/a
31	POLR2A	chr1:46744225-46747381	K562	blood:	n/a	n/a
32	POLR2A	chr1:46737870-46747540	GM12892	blood:	n/a	n/a
33	POLR2A	chr1:46743290-46747430	HL-60	blood:	n/a	n/a
34	POLR2A	chr1:46744424-46747441	K562	blood:	n/a	n/a
35	POLR2A	chr1:46745539-46747324	HepG2	liver:	n/a	n/a
36	POLR2A	chr1:46743516-46747446	PANC-1	pancreas:	n/a	n/a
37	POLR2A	chr1:46737894-46747566	GM12892	blood:	n/a	n/a
38	POLR2A	chr1:46741632-46747555	PANC-1	pancreas:	n/a	n/a

No data

(count:1 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:46711860..46716156-chr1:46745879..46749297,4	K562	blood:

No data

Variant related genes	Relation type
LRRC41	TF binding region
ENSG00000085999	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12137934	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12146051	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17361887	1.00[CHB][hapmap]
rs2019996	0.84[EUR][1000 genomes]
rs55707872	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6658556	1.00[CHB][hapmap]
rs6662982	1.00[CHB][hapmap]
rs6696284	1.00[CHB][hapmap]
rs6697623	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7533750	1.00[CHB][hapmap]
rs7555458	1.00[CHB][hapmap]
rs9429187	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv470711	chr1:46660295-46810530	Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	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

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs12142240	NSUN4	cis	multi-tissue	Pritchard
rs12142240	NSUN4	cis	Muscle Skeletal	GTEx
rs12142240	hmm8232	cis	multi-tissue	Pritchard
rs12142240	NSUN4	cis	cerebellum	SCAN
rs12142240	NSUN4	Cis_1M	lymphoblastoid	RTeQTL
rs12142240	NSUN4	cis	lymphoblastoid	seeQTL
rs12142240	RP5-1109J22.1	cis	Thyroid	GTEx
rs12142240	NSUN4	cis	Whole Blood	GTEx
rs12142240	FAAH	cis	Whole Blood	GTEx
rs12142240	FAAH	cis	cerebellum	SCAN
rs12142240	NSUN4	cis	parietal	SCAN
rs12142240	FAAH	cis	Esophagus Muscularis	GTEx
rs12142240	SNORD55	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46714400-46754200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:46714600-46748600	Strong transcription	HUES48 Cell Line	embryonic stem cell
3	chr1:46714600-46749600	Weak transcription	Fetal Heart	heart
4	chr1:46714800-46748400	Strong transcription	HUES6 Cell Line	embryonic stem cell
5	chr1:46715000-46752800	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr1:46715200-46748000	Strong transcription	H1 Cell Line	embryonic stem cell
7	chr1:46715200-46748400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr1:46715200-46764200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr1:46715400-46748200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr1:46715400-46748400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
11	chr1:46715400-46748400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr1:46715400-46753000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr1:46715400-46754200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr1:46715400-46763800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr1:46715400-46764400	Strong transcription	Cortex derived primary cultured neurospheres	brain
16	chr1:46715400-46765600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:46716000-46749400	Strong transcription	Fetal Thymus	thymus
18	chr1:46717200-46748000	Strong transcription	Thymus	Thymus
19	chr1:46718200-46749600	Strong transcription	Dnd41	blood
20	chr1:46720600-46750800	Strong transcription	Fetal Muscle Trunk	muscle
21	chr1:46720800-46766400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr1:46721600-46753800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr1:46721800-46750600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr1:46723200-46755200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr1:46724200-46756000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr1:46725400-46748000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
27	chr1:46726200-46747800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr1:46728600-46751000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr1:46730000-46764000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr1:46733600-46766200	Weak transcription	Small Intestine	intestine
31	chr1:46734000-46748400	Strong transcription	A549	lung
32	chr1:46736400-46752400	Strong transcription	Primary hematopoietic stem cells	blood
33	chr1:46738400-46750200	Strong transcription	Fetal Intestine Large	intestine
34	chr1:46738400-46752200	Strong transcription	GM12878-XiMat	blood
35	chr1:46740400-46753800	Strong transcription	NH-A	brain
36	chr1:46741200-46755000	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr1:46741600-46763400	Strong transcription	Fetal Stomach	stomach
38	chr1:46741800-46749600	Strong transcription	Fetal Muscle Leg	muscle
39	chr1:46741800-46749800	Strong transcription	Fetal Intestine Small	intestine
40	chr1:46742000-46750400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr1:46742000-46751200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr1:46742000-46753800	Strong transcription	Brain Germinal Matrix	brain
43	chr1:46742200-46750400	Strong transcription	Osteobl	bone
44	chr1:46742200-46754400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr1:46742600-46756000	Strong transcription	Duodenum Mucosa	Duodenum
46	chr1:46742800-46747400	Strong transcription	NHLF	lung
47	chr1:46742800-46748200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr1:46742800-46748600	Strong transcription	Fetal Brain Female	brain
49	chr1:46742800-46748800	Strong transcription	Brain Angular Gyrus	brain
50	chr1:46742800-46751000	Strong transcription	HSMM	muscle

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