Variant report

Variant	rs9878498
Chromosome Location	chr3:139397399-139397400
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:61)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAZ	chr3:139395661-139397413	K562	blood:	n/a	chr3:139396474-139396485 chr3:139396470-139396489 chr3:139396475-139396484 chr3:139396477-139396486

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:139397363-139397413	ProgFib	skin:	n/a
2	chr3:139397363-139397413	GM12878	blood:	n/a
3	chr3:139397363-139397413	T-47D	breast:	n/a
4	chr3:139397363-139397413	HCF	heart:	n/a
5	chr3:139397363-139397413	SK-N-MC	brain:	n/a
6	chr3:139397363-139397413	A549	lung:	n/a
7	chr3:139397363-139397413	Caco-2	colon:	n/a
8	chr3:139397363-139397413	HCM	heart:	n/a
9	chr3:139397363-139397413	AoSMC	blood vessel:	n/a
10	chr3:139397363-139397413	HL-60	blood:	n/a
11	chr3:139397363-139397413	GM19239	blood:	n/a
12	chr3:139397363-139397413	PANC-1	pancreas:	n/a
13	chr3:139397363-139397413	HPAEpiC	pulmonary alveolar:	n/a
14	chr3:139397363-139397413	AG09309	skin:	n/a
15	chr3:139397363-139397413	SK-N-SH_RA	brain:	n/a
16	chr3:139397363-139397413	SKMC	muscle:	n/a
17	chr3:139397363-139397413	HEEpiC	esophagus:	n/a
18	chr3:139397363-139397413	NB4	blood:	n/a
19	chr3:139397363-139397413	GM12892	blood:	n/a
20	chr3:139397363-139397413	HEK293	kidney:	embryo
21	chr3:139397363-139397413	HNPCEpiC	eye:	n/a
22	chr3:139397363-139397413	SK-N-SH	brain:	n/a
23	chr3:139397363-139397413	RPTEC	kidney:	n/a
24	chr3:139397363-139397413	BE2_C	brain:	n/a
25	chr3:139397363-139397413	AG04449	skin:	fetal
26	chr3:139397363-139397413	NH-A	brain:	n/a
27	chr3:139397363-139397413	ovcar-3	ovarian:	n/a
28	chr3:139397363-139397413	HUVEC	blood vessel:	n/a
29	chr3:139397363-139397413	PrEC	prostate:	n/a
30	chr3:139397363-139397413	NHDF-neo	bronchial:	n/a
31	chr3:139397363-139397413	PFSK-1	brain:	n/a
32	chr3:139397363-139397413	MCF10A-Er-Src	breast:	n/a
33	chr3:139397363-139397413	HRE	kidney:	n/a
34	chr3:139397363-139397413	GM06990	blood:	n/a
35	chr3:139397363-139397413	HMEC	breast:	n/a
36	chr3:139397363-139397413	AG10803	skin:	n/a
37	chr3:139397363-139397413	CMK	blood:	n/a
38	chr3:139397363-139397413	NT2-D1	testis:	n/a
39	chr3:139397363-139397413	BJ	skin:	n/a
40	chr3:139397363-139397413	Hepatocyte	liver:	n/a
41	chr3:139397363-139397413	GM12891	blood:	n/a
42	chr3:139397363-139397413	Hela-S3	cervix:	n/a
43	chr3:139397363-139397413	HCT-116	colon:	n/a
44	chr3:139397363-139397413	NHBE	bronchial:	n/a
45	chr3:139397363-139397413	HIPEpiC	eye:	n/a
46	chr3:139397363-139397413	SAEC	small airway:	n/a
47	chr3:139397363-139397413	Jurkat	blood:	n/a
48	chr3:139397363-139397413	HAEpiC	amniotic membrane:	n/a
49	chr3:139397363-139397413	H1-hESC	embryonic stem cell:	embryo
50	chr3:139397363-139397413	HRCEpiC	kidney:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:139395742..139397404-chr3:139400797..139402363,2	K562	blood:
2	chr3:139396870..139399383-chr3:139403869..139405785,2	K562	blood:

No data

Variant related genes	Relation type
NMNAT3	TF binding region
NMNAT3	CpG island
ENSG00000261763	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10935341	0.96[ASN][1000 genomes]
rs12186041	1.00[ASN][1000 genomes]
rs12632145	0.90[ASN][1000 genomes]
rs12634170	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13074121	0.99[ASN][1000 genomes]
rs16849303	0.99[ASN][1000 genomes]
rs16849305	0.99[ASN][1000 genomes]
rs16849307	0.99[ASN][1000 genomes]
rs16849309	1.00[ASN][1000 genomes]
rs35449667	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35657101	1.00[ASN][1000 genomes]
rs3922940	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4474999	0.84[ASN][1000 genomes]
rs4518082	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4535184	1.00[ASN][1000 genomes]
rs4549242	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4615039	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56711752	0.99[ASN][1000 genomes]
rs57304307	1.00[ASN][1000 genomes]
rs59476496	0.94[ASN][1000 genomes]
rs62270189	0.90[ASN][1000 genomes]
rs62270193	0.90[ASN][1000 genomes]
rs62273120	0.97[ASN][1000 genomes]
rs62273121	0.97[ASN][1000 genomes]
rs62273122	0.94[ASN][1000 genomes]
rs6808215	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71627866	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7617537	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7636269	1.00[ASN][1000 genomes]
rs7651551	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9289581	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9810042	0.98[ASN][1000 genomes]
rs9810049	1.00[ASN][1000 genomes]
rs9815708	1.00[ASN][1000 genomes]
rs9833539	0.99[ASN][1000 genomes]
rs9836944	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9848375	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9865942	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9871543	1.00[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:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139395800-139397400	Active TSS	Brain Cingulate Gyrus	brain
2	chr3:139395800-139397400	Active TSS	Right Atrium	heart
3	chr3:139395800-139397800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
4	chr3:139396000-139397400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
5	chr3:139396000-139397400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
6	chr3:139396000-139397400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
7	chr3:139396000-139397400	Active TSS	Fetal Brain Female	brain
8	chr3:139396200-139397400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
9	chr3:139396200-139397400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
10	chr3:139396200-139397400	Active TSS	Breast Myoepithelial Primary Cells	Breast
11	chr3:139396200-139397400	Active TSS	Fetal Intestine Small	intestine
12	chr3:139396200-139397800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr3:139396400-139397400	Active TSS	H9 Cell Line	embryonic stem cell
14	chr3:139396400-139397400	Active TSS	Brain Anterior Caudate	brain
15	chr3:139396400-139397400	Active TSS	Skeletal Muscle Male	skeletal muscle
16	chr3:139396400-139397600	Active TSS	Primary T helper cells PMA-I stimulated	--
17	chr3:139396400-139397600	Active TSS	Rectal Smooth Muscle	rectum
18	chr3:139396400-139397800	Active TSS	Colon Smooth Muscle	Colon
19	chr3:139396600-139397400	Active TSS	HUES48 Cell Line	embryonic stem cell
20	chr3:139396800-139397400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr3:139396800-139397400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
22	chr3:139396800-139397400	Active TSS	Adipose Nuclei	Adipose
23	chr3:139396800-139397400	Active TSS	Monocytes-CD14+_RO01746	blood
24	chr3:139396800-139397600	Active TSS	Primary hematopoietic stem cells	blood
25	chr3:139397000-139397400	Enhancers	Rectal Mucosa Donor 31	rectum
26	chr3:139397000-139397600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
27	chr3:139397000-139397600	Enhancers	Primary T killer memory cells from peripheral blood	blood
28	chr3:139397000-139397600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr3:139397000-139397600	Flanking Active TSS	Stomach Smooth Muscle	stomach
30	chr3:139397000-139397800	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr3:139397000-139406800	Weak transcription	Psoas Muscle	Psoas
32	chr3:139397200-139397400	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
33	chr3:139397200-139397400	Active TSS	Primary B cells from cord blood	blood
34	chr3:139397200-139397400	Flanking Active TSS	Primary T cells from cord blood	blood
35	chr3:139397200-139397400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
36	chr3:139397200-139397400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
37	chr3:139397200-139397400	Flanking Active TSS	Brain Germinal Matrix	brain
38	chr3:139397200-139397400	Enhancers	Brain Substantia Nigra	brain
39	chr3:139397200-139397400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
40	chr3:139397200-139397400	Enhancers	Fetal Stomach	stomach
41	chr3:139397200-139397400	Enhancers	Fetal Thymus	thymus
42	chr3:139397200-139397400	Flanking Active TSS	Thymus	Thymus
43	chr3:139397200-139397600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
44	chr3:139397200-139397600	Enhancers	Primary B cells from peripheral blood	blood
45	chr3:139397200-139397600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr3:139397200-139397600	Enhancers	Primary T helper cells fromperipheralblood	blood
47	chr3:139397200-139397600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr3:139397200-139397600	Bivalent Enhancer	Fetal Muscle Leg	muscle
49	chr3:139397200-139397800	Enhancers	H1 Cell Line	embryonic stem cell
50	chr3:139397200-139397800	Enhancers	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links