Variant report

Variant	rs4128707
Chromosome Location	chr12:58288363-58288364
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:3)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr12:58288260-58288410	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr12:58287306-58288398	SK-N-SH	brain:	n/a	n/a
3	NFIC	chr12:58287215-58288417	SK-N-SH	brain:	n/a	n/a
4	GATA3	chr12:58287156-58288386	SK-N-SH	brain:	n/a	chr12:58287479-58287487
5	TCF12	chr12:58287159-58288441	SK-N-SH	brain:	n/a	chr12:58287174-58287182 chr12:58287272-58287280

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:58283503..58285277-chr12:58287800..58289369,2	K562	blood:
2	chr12:58238695..58240382-chr12:58287823..58289916,2	K562	blood:
3	chr12:58236711..58242486-chr12:58286970..58293951,15	MCF-7	breast:
4	chr12:58233944..58243826-chr12:58273095..58290464,46	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CTDSP2-1	chr12:58287523-58290265	ENSG00000245651
2	lnc-CTDSP2-1	chr12:58287523-58290267	XLOC_010101
3	lnc-CTDSP2-1	chr12:58287523-58290265	ENSG00000245651

No data

Variant related genes	Relation type
ENSG00000245651	TF binding region
ENSG00000175215	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10747786	0.90[CHD][hapmap]
rs10747787	0.90[CHD][hapmap]
rs10877029	0.90[CHD][hapmap]
rs10877030	0.90[CHD][hapmap]
rs10877033	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10877034	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11172367	0.87[CHD][hapmap]
rs11172371	0.88[CHB][hapmap];0.83[ASN][1000 genomes]
rs11172372	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11172375	0.81[ASN][1000 genomes]
rs11172378	0.88[CHB][hapmap];0.93[CHD][hapmap];0.83[ASN][1000 genomes]
rs1962047	0.88[CHB][hapmap];0.97[CHD][hapmap];0.83[ASN][1000 genomes]
rs2002275	0.88[CHB][hapmap];0.97[CHD][hapmap];0.81[ASN][1000 genomes]
rs3751330	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3751331	0.83[ASN][1000 genomes]
rs4237844	0.87[CHD][hapmap]
rs4237845	0.81[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4417327	0.95[ASN][1000 genomes]
rs4553410	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4630335	0.83[CHB][hapmap];0.87[CHD][hapmap]
rs4760172	0.87[CHD][hapmap]
rs4760340	0.81[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];0.81[ASN][1000 genomes]
rs6581157	0.83[ASN][1000 genomes]
rs6650217	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6650218	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6650219	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7306124	0.81[ASN][1000 genomes]
rs7312623	0.90[CHD][hapmap]
rs7954591	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7954957	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7963992	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7971877	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv559046	chr12:58162085-58478598	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	261 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4128707	XRCC6BP1	cis	lymphoblastoid	seeQTL
rs4128707	XRCC6BP1	cis	multi-tissue	Pritchard
rs4128707	NCKAP1L	cis	cerebellum	SCAN
rs4128707	DKFZP586D0919	cis	multi-tissue	Pritchard

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58281600-58288400	Enhancers	K562	blood
2	chr12:58282200-58289600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr12:58283200-58288400	Weak transcription	Primary T cells from cord blood	blood
4	chr12:58283200-58288400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr12:58283400-58288400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr12:58285600-58290000	Enhancers	Brain Angular Gyrus	brain
7	chr12:58285600-58290000	Enhancers	Left Ventricle	heart
8	chr12:58285600-58290200	Enhancers	Sigmoid Colon	Sigmoid Colon
9	chr12:58285800-58289600	Enhancers	Duodenum Mucosa	Duodenum
10	chr12:58285800-58289800	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr12:58285800-58290000	Enhancers	Placenta	Placenta
12	chr12:58285800-58290000	Enhancers	Right Atrium	heart
13	chr12:58285800-58290000	Enhancers	Right Ventricle	heart
14	chr12:58285800-58290200	Enhancers	Lung	lung
15	chr12:58286000-58289800	Enhancers	Stomach Mucosa	stomach
16	chr12:58286000-58290600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr12:58286200-58289400	Enhancers	Brain Cingulate Gyrus	brain
18	chr12:58286200-58290000	Enhancers	Fetal Thymus	thymus
19	chr12:58286400-58289800	Enhancers	Brain Substantia Nigra	brain
20	chr12:58286600-58288400	Enhancers	Primary neutrophils fromperipheralblood	blood
21	chr12:58286600-58288400	Weak transcription	Esophagus	oesophagus
22	chr12:58286600-58289600	Enhancers	Fetal Brain Female	brain
23	chr12:58286600-58290200	Enhancers	Placenta Amnion	Placenta Amnion
24	chr12:58286800-58289800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr12:58286800-58291400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr12:58287000-58288400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr12:58287000-58288400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr12:58287000-58288400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr12:58287000-58288400	Enhancers	A549	lung
30	chr12:58287000-58288600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
31	chr12:58287000-58288600	Flanking Active TSS	Stomach Smooth Muscle	stomach
32	chr12:58287000-58289600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr12:58287000-58289600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr12:58287000-58290000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr12:58287200-58288400	Enhancers	H1 Cell Line	embryonic stem cell
36	chr12:58287200-58288400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr12:58287200-58288400	Flanking Active TSS	Fetal Intestine Small	intestine
38	chr12:58287200-58288400	Enhancers	HMEC	breast
39	chr12:58287200-58288400	Enhancers	HSMM	muscle
40	chr12:58287200-58288400	Enhancers	HUVEC	blood vessel
41	chr12:58287200-58288400	Flanking Active TSS	Osteobl	bone
42	chr12:58287200-58288600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr12:58287200-58288600	Enhancers	HUES64 Cell Line	embryonic stem cell
44	chr12:58287200-58288600	Enhancers	Primary monocytes fromperipheralblood	blood
45	chr12:58287200-58288600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr12:58287200-58288600	Flanking Active TSS	Brain Germinal Matrix	brain
47	chr12:58287200-58288600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
48	chr12:58287200-58288800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr12:58287200-58289200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
50	chr12:58287200-58290000	Enhancers	Primary hematopoietic stem cells short term culture	blood

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