Variant report

Variant	rs881744
Chromosome Location	chr4:53727487-53727488
allele	A/G
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	E2F6	chr4:53727459-53729023	H1-hESC	embryonic stem cell:	n/a	chr4:53728200-53728210 chr4:53728643-53728654 chr4:53728435-53728444 chr4:53728439-53728449
2	SIN3A	chr4:53726721-53729851	H1-hESC	embryonic stem cell:	n/a	n/a
3	MXI1	chr4:53726951-53732052	SK-N-SH	brain:	n/a	n/a
4	CTBP2	chr4:53727338-53729596	H1-hESC	embryonic stem cell:	n/a	n/a
5	RAD21	chr4:53727407-53729218	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:53525430..53527688-chr4:53726700..53729187,4	MCF-7	breast:
2	chr4:53723992..53727784-chr4:53728716..53731112,4	K562	blood:
3	chr4:53577401..53580169-chr4:53726393..53730142,5	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SCFD2-2	chr4:53727309-53727898	NONHSAT096385

Variant related genes	Relation type
RASL11B	TF binding region
ENSG00000226950	Chromatin interaction
ENSG00000128045	Chromatin interaction
ENSG00000212588	Chromatin interaction
ENSG00000248866	Chromatin interaction
ENSG00000109189	Chromatin interaction
ENSG00000264585	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10517269	0.85[CHB][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.89[MEX][hapmap];0.90[YRI][hapmap];0.91[AMR][1000 genomes]
rs1109696	0.89[YRI][hapmap]
rs11932601	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap]
rs11938159	0.82[CHB][hapmap];0.85[JPT][hapmap];0.94[YRI][hapmap];0.98[AMR][1000 genomes]
rs11939448	0.85[CHB][hapmap];0.85[JPT][hapmap];0.88[YRI][hapmap];0.95[AMR][1000 genomes]
rs17082074	0.80[ASN][1000 genomes]
rs17082084	0.81[YRI][hapmap]
rs17082087	0.82[AMR][1000 genomes]
rs17082091	0.87[AMR][1000 genomes]
rs2007936	0.89[YRI][hapmap]
rs2007959	0.89[YRI][hapmap]
rs3811781	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs41279517	0.95[ASN][1000 genomes]
rs58461944	0.82[AMR][1000 genomes]
rs58577680	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs59042894	0.87[AMR][1000 genomes]
rs6554054	0.89[AMR][1000 genomes]
rs6554057	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6817433	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6818178	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6838718	0.92[ASW][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6848200	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6858566	0.85[YRI][hapmap]
rs73814868	0.91[AMR][1000 genomes]
rs73814875	0.90[ASN][1000 genomes]
rs73814883	0.95[ASN][1000 genomes]
rs73814886	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7655781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7663419	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7670068	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7685816	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7688141	1.00[CEU][hapmap];0.82[JPT][hapmap];0.84[YRI][hapmap];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7693568	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7699960	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.82[MEX][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[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	nsv594201	chr4:52798624-53732445	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1004889	chr4:53436500-54106281	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv537094	chr4:53436500-54106281	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv1004086	chr4:53698581-53773183	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv3360858	chr4:53727420-53729968	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs881744	CR2	trans	lymphoblastoid	seeQTL

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:53720600-53727800	Weak transcription	Aorta	Aorta
2	chr4:53720600-53728000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr4:53722400-53727600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr4:53723600-53727600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr4:53725800-53727600	Enhancers	Fetal Brain Male	brain
6	chr4:53726000-53727800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr4:53726200-53727600	Enhancers	H1 Cell Line	embryonic stem cell
8	chr4:53726800-53727600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr4:53726800-53728000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr4:53726800-53728000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
11	chr4:53727000-53727600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
12	chr4:53727200-53727600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr4:53727200-53727600	Enhancers	Fetal Brain Female	brain
14	chr4:53727200-53727800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr4:53727200-53727800	Bivalent Enhancer	Fetal Muscle Leg	muscle
16	chr4:53727200-53728000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
17	chr4:53727200-53728000	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
18	chr4:53727200-53728200	Flanking Active TSS	Fetal Heart	heart
19	chr4:53727400-53727600	Flanking Active TSS	H9 Cell Line	embryonic stem cell
20	chr4:53727400-53727600	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr4:53727400-53727600	Active TSS	iPS-15b Cell Line	embryonic stem cell
22	chr4:53727400-53727600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr4:53727400-53727600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr4:53727400-53727600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr4:53727400-53727600	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr4:53727400-53727600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr4:53727400-53727600	Enhancers	Brain Anterior Caudate	brain
28	chr4:53727400-53727600	Enhancers	Brain Cingulate Gyrus	brain
29	chr4:53727400-53727600	Enhancers	Brain Hippocampus Middle	brain
30	chr4:53727400-53727600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
31	chr4:53727400-53727600	Enhancers	Ovary	ovary
32	chr4:53727400-53727800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr4:53727400-53727800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr4:53727400-53727800	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr4:53727400-53727800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr4:53727400-53727800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
37	chr4:53727400-53727800	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
38	chr4:53727400-53727800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
39	chr4:53727400-53727800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
40	chr4:53727400-53727800	Bivalent Enhancer	Fetal Stomach	stomach
41	chr4:53727400-53727800	Bivalent Enhancer	Fetal Thymus	thymus
42	chr4:53727400-53727800	Enhancers	Gastric	stomach
43	chr4:53727400-53727800	Bivalent Enhancer	GM12878-XiMat	blood
44	chr4:53727400-53728000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr4:53727400-53728000	Enhancers	Spleen	Spleen
46	chr4:53727400-53728200	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr4:53727400-53729600	Active TSS	Brain Angular Gyrus	brain
48	chr4:53727400-53729600	Active TSS	Brain Inferior Temporal Lobe	brain

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