Variant report

Variant	rs3821543
Chromosome Location	chr3:139252062-139252063
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:139251954..139254660-chr3:139259598..139262357,2	MCF-7	breast:
2	chr3:139251496..139253555-chr3:139254279..139256942,2	MCF-7	breast:
3	chr3:139245782..139250222-chr3:139250781..139254846,5	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1116748	0.87[EUR][1000 genomes]
rs11549984	0.93[EUR][1000 genomes]
rs12489687	0.93[EUR][1000 genomes]
rs12493507	0.92[CEU][hapmap];0.93[EUR][1000 genomes]
rs1391029	0.93[EUR][1000 genomes]
rs1391030	0.93[EUR][1000 genomes]
rs1391031	0.93[EUR][1000 genomes]
rs1511570	0.92[CEU][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs1511571	0.93[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs17337746	0.93[EUR][1000 genomes]
rs17397112	0.93[EUR][1000 genomes]
rs2011770	0.93[EUR][1000 genomes]
rs3772868	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4270469	0.93[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs4407373	0.91[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs4683502	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55641400	0.93[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs55642746	0.93[EUR][1000 genomes]
rs55724241	0.93[EUR][1000 genomes]
rs55780517	0.93[EUR][1000 genomes]
rs55817881	0.93[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs55834130	0.93[EUR][1000 genomes]
rs55968289	0.93[EUR][1000 genomes]
rs55987999	0.93[EUR][1000 genomes]
rs56034427	0.93[EUR][1000 genomes]
rs56051054	0.93[EUR][1000 genomes]
rs56051514	0.93[EUR][1000 genomes]
rs56058641	0.93[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs56170893	0.93[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs56210757	0.87[EUR][1000 genomes]
rs56343214	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57459746	0.93[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs73220932	0.93[EUR][1000 genomes]
rs73220940	0.93[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs73220941	0.93[EUR][1000 genomes]
rs73220944	0.91[EUR][1000 genomes]
rs893703	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs930412	0.93[AFR][1000 genomes];0.92[EUR][1000 genomes]

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	nsv877543	chr3:139021139-139327261	Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv1003154	chr3:139060841-139788752	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv536729	chr3:139060841-139788752	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv949635	chr3:139091219-139367043	Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv916193	chr3:139187767-139821526	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv530058	chr3:139243971-139814419	Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139228800-139253200	Weak transcription	Gastric	stomach
2	chr3:139231000-139252800	Weak transcription	Right Ventricle	heart
3	chr3:139234400-139252600	Weak transcription	Lung	lung
4	chr3:139235000-139253600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr3:139241400-139253200	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr3:139243800-139252600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr3:139247400-139252600	Weak transcription	Aorta	Aorta
8	chr3:139248400-139252200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr3:139248400-139252600	Weak transcription	NHEK	skin
10	chr3:139248600-139252400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr3:139249600-139254400	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr3:139249600-139255000	Enhancers	Pancreas	Pancrea
13	chr3:139249600-139256400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
14	chr3:139249800-139252600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:139249800-139253800	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr3:139249800-139257400	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr3:139250000-139252600	Enhancers	Brain Hippocampus Middle	brain
18	chr3:139250000-139256600	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr3:139250200-139255000	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr3:139250200-139255000	Enhancers	Brain Anterior Caudate	brain
21	chr3:139250400-139252600	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr3:139250400-139252600	Weak transcription	Esophagus	oesophagus
23	chr3:139250600-139254600	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr3:139250600-139254600	Enhancers	Fetal Lung	lung
25	chr3:139250600-139255400	Enhancers	Brain Angular Gyrus	brain
26	chr3:139250600-139256800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr3:139250800-139254400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr3:139250800-139257400	Enhancers	Brain Cingulate Gyrus	brain
29	chr3:139251000-139252800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr3:139251000-139252800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr3:139251000-139253200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr3:139251000-139254600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr3:139251000-139255800	Enhancers	Fetal Kidney	kidney
34	chr3:139251200-139254200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr3:139251200-139254400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
36	chr3:139251200-139254600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr3:139251200-139254600	Enhancers	Fetal Intestine Large	intestine
38	chr3:139251200-139255800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:139251200-139257400	Genic enhancers	Fetal Intestine Small	intestine
40	chr3:139251400-139253000	Weak transcription	Spleen	Spleen
41	chr3:139251400-139253400	Enhancers	Fetal Stomach	stomach
42	chr3:139251400-139254200	Enhancers	HepG2	liver
43	chr3:139251400-139255400	Enhancers	Placenta	Placenta
44	chr3:139251400-139256400	Enhancers	Liver	Liver
45	chr3:139251400-139257200	Enhancers	Duodenum Mucosa	Duodenum
46	chr3:139251600-139252200	Enhancers	HUES64 Cell Line	embryonic stem cell
47	chr3:139251600-139252200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr3:139251600-139252800	Enhancers	Duodenum Smooth Muscle	Duodenum
49	chr3:139251600-139252800	Enhancers	Psoas Muscle	Psoas
50	chr3:139251600-139253000	Enhancers	Small Intestine	intestine

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