Variant report

Variant	rs883739
Chromosome Location	chr3:46538018-46538019
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr3:46537241-46539044	IMR90	lung:	n/a	n/a
2	CTCF	chr3:46537980-46538130	AG09319	gingival:	n/a	n/a
3	CTCF	chr3:46537900-46538050	AG04450	lung:	n/a	n/a
4	CTCF	chr3:46538000-46538150	HMF	breast:	n/a	n/a
5	CEBPB	chr3:46537310-46538028	IMR90	lung:	n/a	n/a
6	CTCF	chr3:46538000-46538150	NB4	blood:	n/a	n/a
7	UBTF	chr3:46538008-46538048	K562	blood:	n/a	n/a
8	ZNF274	chr3:46537658-46538225	K562	blood:	n/a	n/a
9	TCF12	chr3:46537546-46538098	SK-N-SH	brain:	n/a	n/a
10	CTCF	chr3:46537940-46538090	GM12864	blood:	n/a	n/a
11	TCF12	chr3:46537442-46538170	SK-N-SH	brain:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr3:46537907..46538428-chr3:46599296..46599996,2	K562	blood:
2	chr3:46537971..46538930-chr3:46599529..46600154,4	MCF-7	breast:
3	chr3:46537655..46538429-chr3:46599459..46599986,2	MCF-7	breast:

No data

Variant related genes	Relation type
RTP3	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10514713	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10865941	0.96[CEU][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap]
rs10865942	0.81[AMR][1000 genomes]
rs11130093	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11130094	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11714743	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11719033	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12489007	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12489117	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12490169	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12496623	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12496864	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1402151	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1520483	1.00[CEU][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap]
rs17030627	0.81[CHD][hapmap]
rs2037391	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2139634	0.80[EUR][1000 genomes]
rs2280407	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28413725	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3934896	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60986461	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6763280	0.80[EUR][1000 genomes]
rs6791703	0.84[YRI][hapmap]
rs885485	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs885486	1.00[CEU][hapmap];0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014624	chr3:46463424-46549188	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
2	nsv1013306	chr3:46469014-46698538	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv1009892	chr3:46496775-46546918	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	nsv536553	chr3:46496775-46546918	Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs883739	NPRL2	cis	parietal	SCAN
rs883739	LTF	cis	parietal	SCAN
rs883739	C3orf45	cis	parietal	SCAN
rs883739	LRRC2	cis	parietal	SCAN
rs883739	JPH1	trans	cerebellum	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46530800-46538600	Weak transcription	Pancreas	Pancrea
2	chr3:46531000-46538400	Weak transcription	Lung	lung
3	chr3:46531200-46541600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:46531400-46540200	Weak transcription	Left Ventricle	heart
5	chr3:46532400-46538400	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr3:46532400-46538400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr3:46533000-46538400	Weak transcription	Right Ventricle	heart
8	chr3:46533000-46544200	Weak transcription	Psoas Muscle	Psoas
9	chr3:46534600-46538400	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr3:46535000-46538600	Weak transcription	Fetal Intestine Large	intestine
11	chr3:46537200-46538200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr3:46537200-46538200	Enhancers	Muscle Satellite Cultured Cells	--
13	chr3:46537200-46538200	Enhancers	HMEC	breast
14	chr3:46537200-46538200	Enhancers	HSMM	muscle
15	chr3:46537200-46538200	Enhancers	HSMMtube	muscle
16	chr3:46537200-46538200	Enhancers	NHEK	skin
17	chr3:46537200-46538200	Enhancers	NHLF	lung
18	chr3:46537200-46538400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr3:46537200-46538400	Enhancers	Liver	Liver
20	chr3:46537200-46538400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr3:46537200-46538600	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr3:46537200-46538600	Enhancers	iPS-20b Cell Line	embryonic stem cell
23	chr3:46537200-46538600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr3:46537200-46538600	Enhancers	NH-A	brain
25	chr3:46537200-46538600	Enhancers	NHDF-Ad	bronchial
26	chr3:46537200-46538800	Enhancers	HUES64 Cell Line	embryonic stem cell
27	chr3:46537200-46538800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr3:46537200-46538800	Enhancers	Osteobl	bone
29	chr3:46537200-46539000	Enhancers	HUES48 Cell Line	embryonic stem cell
30	chr3:46537200-46539000	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr3:46537200-46539200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr3:46537200-46540000	Enhancers	Dnd41	blood
33	chr3:46537200-46546200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr3:46537200-46547000	Enhancers	Fetal Thymus	thymus
35	chr3:46537200-46550200	Enhancers	K562	blood
36	chr3:46537400-46538200	Enhancers	iPS-18 Cell Line	embryonic stem cell
37	chr3:46537400-46538200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr3:46537400-46538200	Enhancers	Colon Smooth Muscle	Colon
39	chr3:46537400-46538200	Enhancers	Stomach Smooth Muscle	stomach
40	chr3:46537400-46538800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr3:46537400-46539000	Enhancers	HUVEC	blood vessel
42	chr3:46537400-46539600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr3:46537400-46542000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr3:46537600-46538200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr3:46537600-46538400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr3:46537600-46538400	Weak transcription	Spleen	Spleen
47	chr3:46537600-46538800	Enhancers	Right Atrium	heart
48	chr3:46537600-46539400	Enhancers	Adipose Nuclei	Adipose
49	chr3:46538000-46538800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
50	chr3:46538000-46538800	Enhancers	Primary T killer memory cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links