Variant report

Variant	rs10935483
Chromosome Location	chr3:142890392-142890393
allele	C/T
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	EBF1	chr3:142889853-142890441	GM12878	blood:	n/a	n/a
2	RUNX3	chr3:142889632-142890530	GM12878	blood:	n/a	n/a
3	EP300	chr3:142890006-142890462	GM12878	blood:	n/a	chr3:142890344-142890353
4	ELK1	chr3:142890048-142890444	GM12878	blood:	n/a	n/a
5	RUNX3	chr3:142890011-142890449	GM12878	blood:	n/a	n/a
6	BCLAF1	chr3:142889996-142890544	GM12878	blood:	n/a	n/a
7	NFIC	chr3:142889934-142890467	GM12878	blood:	n/a	n/a
8	POLR2A	chr3:142889754-142890466	GM12878	blood:	n/a	n/a
9	EP300	chr3:142890098-142890477	GM12878	blood:	n/a	chr3:142890344-142890353
10	STAT3	chr3:142889891-142890511	GM12878	blood:	n/a	chr3:142890347-142890354
11	NFIC	chr3:142889881-142890405	GM12878	blood:	n/a	n/a
12	MAZ	chr3:142889522-142890411	GM12878	blood:	n/a	n/a
13	TBP	chr3:142889555-142890489	GM12878	blood:	n/a	n/a
14	EP300	chr3:142889975-142890430	GM12878	blood:	n/a	chr3:142890344-142890353
15	MXI1	chr3:142889988-142890478	GM12878	blood:	n/a	n/a
16	SMC3	chr3:142890010-142890495	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:142889368..142891930-chr3:142894381..142895952,2	K562	blood:
2	chr3:142889235..142895118-chr3:142897231..142901814,7	K562	blood:

Variant related genes	Relation type
PBX2P1	TF binding region
ENSG00000244171	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10513192	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12489438	1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12490261	0.81[CHB][hapmap]
rs1449866	0.83[AMR][1000 genomes]
rs1449867	0.81[CHB][hapmap]
rs1530266	0.81[CHB][hapmap];0.81[CHD][hapmap]
rs4683751	1.00[JPT][hapmap]
rs4683756	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4683758	0.81[CHB][hapmap];0.81[CHD][hapmap]
rs56871370	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61739574	0.83[EUR][1000 genomes]
rs67722735	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7649342	0.81[CHB][hapmap];0.81[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757893	chr3:142720230-142962932	Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	esv2759183	chr3:142720230-142964373	Strong transcription Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv949288	chr3:142793323-143585882	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv1007164	chr3:142837004-142891719	Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv508250	chr3:142842454-142943722	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv34280	chr3:142887460-142962075	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142882000-142891600	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr3:142884000-142891600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr3:142884200-142891200	Enhancers	K562	blood
4	chr3:142886600-142890400	Enhancers	Primary T cells fromperipheralblood	blood
5	chr3:142886800-142890400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
6	chr3:142886800-142891400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr3:142887600-142891400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
8	chr3:142887800-142891400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr3:142887800-142891800	Enhancers	Primary B cells from cord blood	blood
10	chr3:142888000-142891200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr3:142888200-142891400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr3:142888200-142891800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr3:142888600-142891600	Flanking Active TSS	Primary T cells from cord blood	blood
14	chr3:142888600-142891800	Enhancers	Primary B cells from peripheral blood	blood
15	chr3:142889000-142890400	Enhancers	HMEC	breast
16	chr3:142889000-142890800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
17	chr3:142889000-142891400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr3:142889000-142891400	Enhancers	NH-A	brain
19	chr3:142889000-142891400	Enhancers	Osteobl	bone
20	chr3:142889000-142891600	Enhancers	Fetal Kidney	kidney
21	chr3:142889000-142891800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr3:142889200-142890400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr3:142889200-142891600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr3:142889200-142891600	Enhancers	Fetal Muscle Leg	muscle
25	chr3:142889200-142891800	Enhancers	Fetal Stomach	stomach
26	chr3:142889200-142891800	Enhancers	NHLF	lung
27	chr3:142889400-142890400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr3:142889400-142890400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
29	chr3:142889400-142890400	Enhancers	Duodenum Mucosa	Duodenum
30	chr3:142889400-142890600	Enhancers	HSMM	muscle
31	chr3:142889400-142890600	Enhancers	HUVEC	blood vessel
32	chr3:142889400-142890800	Flanking Active TSS	GM12878-XiMat	blood
33	chr3:142889400-142891200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr3:142889400-142891200	Enhancers	Muscle Satellite Cultured Cells	--
35	chr3:142889600-142891400	Enhancers	NHDF-Ad	bronchial
36	chr3:142889600-142891600	Enhancers	Primary T killer memory cells from peripheral blood	blood
37	chr3:142889600-142891800	Flanking Active TSS	Fetal Thymus	thymus
38	chr3:142889800-142892000	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr3:142890000-142891000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr3:142890000-142891000	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr3:142890000-142891400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr3:142890000-142891600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr3:142890000-142892000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
44	chr3:142890200-142890400	Enhancers	NHEK	skin
45	chr3:142890200-142890600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr3:142890200-142890600	Enhancers	Dnd41	blood
47	chr3:142890200-142891000	Enhancers	Primary T helper cells PMA-I stimulated	--
48	chr3:142890200-142891000	Enhancers	Fetal Lung	lung
49	chr3:142890200-142891000	Active TSS	Thymus	Thymus
50	chr3:142890200-142891200	Enhancers	Primary T helper naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links