Variant report

Variant	rs11939448
Chromosome Location	chr4:53709479-53709480
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:53707871..53710353-chr4:53715522..53717667,2	MCF-7	breast:
2	chr4:53707171..53710992-chr4:53726798..53730468,4	MCF-7	breast:
3	chr4:53709061..53711670-chr4:53726343..53729125,3	MCF-7	breast:
4	chr4:53576916..53581689-chr4:53705110..53710230,9	MCF-7	breast:
5	chr4:53708530..53710089-chr4:53712453..53715419,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128045	Chromatin interaction
ENSG00000264585	Chromatin interaction
ENSG00000226950	Chromatin interaction
ENSG00000212588	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10517269	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1109696	0.82[YRI][hapmap]
rs11932601	0.85[CHB][hapmap];0.85[JPT][hapmap];0.82[YRI][hapmap]
rs11938159	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17082087	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs17082091	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2007959	0.82[YRI][hapmap]
rs3811781	0.85[AMR][1000 genomes]
rs58461944	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs59042894	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6554054	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6554057	0.86[CHB][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes]
rs6817433	0.86[CHB][hapmap];0.86[JPT][hapmap];0.95[AMR][1000 genomes]
rs6818178	0.85[CHB][hapmap];0.85[JPT][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs6838718	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6848200	0.85[AMR][1000 genomes]
rs6858566	0.85[JPT][hapmap];0.84[YRI][hapmap]
rs73814868	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs73814886	0.83[AMR][1000 genomes]
rs7655781	0.85[JPT][hapmap];0.95[AMR][1000 genomes]
rs7663419	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7670068	0.81[AMR][1000 genomes]
rs7685816	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs7688141	0.81[CEU][hapmap];0.85[YRI][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7693568	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7699960	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs881744	0.85[CHB][hapmap];0.85[JPT][hapmap];0.88[YRI][hapmap];0.95[AMR][1000 genomes]

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	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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:53698800-53710600	Enhancers	HUES6 Cell Line	embryonic stem cell
2	chr4:53700200-53710800	Enhancers	ES-I3 Cell Line	embryonic stem cell
3	chr4:53700400-53709600	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr4:53702400-53709800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr4:53704000-53709600	Enhancers	Left Ventricle	heart
6	chr4:53704000-53710000	Enhancers	Fetal Muscle Leg	muscle
7	chr4:53704200-53709800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr4:53706000-53710000	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr4:53706600-53709600	Enhancers	Fetal Lung	lung
10	chr4:53706800-53710400	Enhancers	Placenta	Placenta
11	chr4:53707800-53709600	Enhancers	Right Ventricle	heart
12	chr4:53707800-53709800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr4:53708000-53710000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr4:53708200-53710000	Enhancers	Fetal Kidney	kidney
15	chr4:53708400-53709600	Weak transcription	HSMMtube	muscle
16	chr4:53708400-53710600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr4:53708400-53710600	Enhancers	Primary B cells from peripheral blood	blood
18	chr4:53708400-53714000	Weak transcription	Fetal Intestine Small	intestine
19	chr4:53708400-53719000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr4:53708600-53710000	Enhancers	Adipose Nuclei	Adipose
21	chr4:53708600-53714000	Weak transcription	Esophagus	oesophagus
22	chr4:53708600-53714000	Weak transcription	Pancreas	Pancrea
23	chr4:53708600-53718000	Weak transcription	Lung	lung
24	chr4:53708800-53710400	Enhancers	Spleen	Spleen
25	chr4:53709000-53709600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr4:53709000-53709600	Enhancers	iPS-15b Cell Line	embryonic stem cell
27	chr4:53709000-53710200	Enhancers	Primary B cells from cord blood	blood
28	chr4:53709000-53710400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr4:53709000-53710600	Enhancers	GM12878-XiMat	blood
30	chr4:53709000-53712800	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr4:53709000-53718200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr4:53709200-53710400	Weak transcription	Brain Hippocampus Middle	brain
33	chr4:53709200-53711200	Enhancers	Monocytes-CD14+_RO01746	blood
34	chr4:53709200-53712400	Weak transcription	Right Atrium	heart
35	chr4:53709200-53714000	Weak transcription	Duodenum Mucosa	Duodenum
36	chr4:53709200-53714000	Weak transcription	Gastric	stomach
37	chr4:53709200-53714000	Weak transcription	Psoas Muscle	Psoas
38	chr4:53709200-53718000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr4:53709200-53718600	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr4:53709200-53718800	Weak transcription	Colon Smooth Muscle	Colon
41	chr4:53709200-53718800	Weak transcription	Stomach Smooth Muscle	stomach
42	chr4:53709400-53710200	Enhancers	Primary hematopoietic stem cells	blood
43	chr4:53709400-53710200	Weak transcription	Ovary	ovary
44	chr4:53709400-53710200	Bivalent Enhancer	K562	blood
45	chr4:53709400-53710400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr4:53709400-53711000	Enhancers	Primary monocytes fromperipheralblood	blood
47	chr4:53709400-53712800	Weak transcription	Stomach Mucosa	stomach
48	chr4:53709400-53716000	Weak transcription	Fetal Heart	heart
49	chr4:53709400-53718400	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr4:53709400-53721000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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