Variant report

Variant	rs3922621
Chromosome Location	chr3:139397901-139397902
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:3)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:139397901-139397951	GM06990	blood:	n/a
2	chr3:139397901-139397951	HCF	heart:	n/a
3	chr3:139397901-139397951	HIPEpiC	eye:	n/a
4	chr3:139397901-139397951	IMR90	lung:	fetal
5	chr3:139397901-139397951	U87	brain:	n/a
6	chr3:139397901-139397951	ECC-1	luminal epithelium:	n/a
7	chr3:139397901-139397951	HMEC	breast:	n/a
8	chr3:139397901-139397951	HRCEpiC	kidney:	n/a
9	chr3:139397901-139397951	ovcar-3	ovarian:	n/a
10	chr3:139397901-139397951	K562	blood:	n/a
11	chr3:139397901-139397951	AG10803	skin:	n/a
12	chr3:139397901-139397951	AG09309	skin:	n/a
13	chr3:139397901-139397951	HAEpiC	amniotic membrane:	n/a
14	chr3:139397901-139397951	Hepatocyte	liver:	n/a
15	chr3:139397901-139397951	CMK	blood:	n/a
16	chr3:139397901-139397951	GM12878	blood:	n/a
17	chr3:139397901-139397951	GM12892	blood:	n/a
18	chr3:139397901-139397951	HPAEpiC	pulmonary alveolar:	n/a
19	chr3:139397901-139397951	PrEC	prostate:	n/a
20	chr3:139397901-139397951	HRE	kidney:	n/a
21	chr3:139397901-139397951	NT2-D1	testis:	n/a
22	chr3:139397901-139397951	AoSMC	blood vessel:	n/a
23	chr3:139397901-139397951	AG04450	lung:	fetal
24	chr3:139397901-139397951	SK-N-SH	brain:	n/a
25	chr3:139397901-139397951	AG04449	skin:	fetal
26	chr3:139397901-139397951	NHBE	bronchial:	n/a
27	chr3:139397901-139397951	HRPEpiC	eye:	n/a
28	chr3:139397901-139397951	BJ	skin:	n/a
29	chr3:139397901-139397951	HL-60	blood:	n/a
30	chr3:139397901-139397951	SAEC	small airway:	n/a
31	chr3:139397901-139397951	HNPCEpiC	eye:	n/a
32	chr3:139397901-139397951	NH-A	brain:	n/a
33	chr3:139397901-139397951	PANC-1	pancreas:	n/a
34	chr3:139397901-139397951	NB4	blood:	n/a
35	chr3:139397901-139397951	NHDF-neo	bronchial:	n/a
36	chr3:139397901-139397951	MCF10A-Er-Src	breast:	n/a
37	chr3:139397901-139397951	SKMC	muscle:	n/a
38	chr3:139397901-139397951	MCF-7	breast:	n/a
39	chr3:139397901-139397951	SK-N-SH_RA	brain:	n/a
40	chr3:139397901-139397951	LNCaP	prostate:	n/a
41	chr3:139397901-139397951	HCM	heart:	n/a
42	chr3:139397901-139397951	BE2_C	brain:	n/a
43	chr3:139397901-139397951	HCPEpiC	choroid plexus:	n/a
44	chr3:139397901-139397951	HUVEC	blood vessel:	n/a
45	chr3:139397901-139397951	Jurkat	blood:	n/a
46	chr3:139397901-139397951	HCT-116	colon:	n/a
47	chr3:139397901-139397951	Caco-2	colon:	n/a
48	chr3:139397901-139397951	HEK293	kidney:	embryo
49	chr3:139397901-139397951	T-47D	breast:	n/a
50	chr3:139397901-139397951	HepG2	liver:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:139396870..139399383-chr3:139403869..139405785,2	K562	blood:

(count:3 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NMNAT3-1	chr3:139397464-139399833	ENSG00000249979
2	lnc-NMNAT3-1	chr3:139397462-139401406	ENSG00000261763.1
3	lnc-NMNAT3-1	chr3:139397462-139399830	NONHSAT092386

No data

Variant related genes	Relation type
NMNAT3	CpG island

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10804669	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10935343	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11714276	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11717254	0.91[ASN][1000 genomes]
rs11720063	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11720212	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11720232	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12492528	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12639448	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28451114	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3856688	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3922941	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4234472	0.94[AFR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4361244	0.93[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs4683678	0.98[AFR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4683680	0.93[AFR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55983509	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59525705	0.94[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62270195	0.91[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7633367	0.93[AFR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9784259	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]

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	nsv1003154	chr3:139060841-139788752	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv536729	chr3:139060841-139788752	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer 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	28 gene(s)	inside rSNPs	diseases
3	nsv916193	chr3:139187767-139821526	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv530058	chr3:139243971-139814419	Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	esv3431059	chr3:139395962-139398210	Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139397000-139406800	Weak transcription	Psoas Muscle	Psoas
2	chr3:139397200-139398600	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr3:139397200-139398800	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr3:139397400-139398200	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
5	chr3:139397400-139406000	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr3:139397600-139398400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr3:139397600-139398600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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