Variant report

Variant	rs73858966
Chromosome Location	chr3:99654183-99654184
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:99653473..99655076-chr3:99658012..99659840,2	MCF-7	breast:
2	chr3:99652546..99654648-chr3:99721251..99724198,2	MCF-7	breast:
3	chr3:99651699..99654533-chr3:99662163..99665139,2	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1038295	0.87[ASN][1000 genomes]
rs10804762	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12485299	0.83[ASN][1000 genomes]
rs12486901	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12489030	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12491153	0.84[EUR][1000 genomes]
rs12493124	0.93[EUR][1000 genomes]
rs1492343	0.83[ASN][1000 genomes]
rs1871847	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35590972	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3732444	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3921767	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4928222	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55874130	0.93[EUR][1000 genomes]
rs55881709	0.89[EUR][1000 genomes]
rs55964918	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56140081	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56223679	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56260910	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56335268	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60119031	0.90[ASN][1000 genomes]
rs61010376	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6792339	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6800456	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73859911	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73860464	0.83[ASN][1000 genomes]
rs73860470	0.86[ASN][1000 genomes]
rs7632345	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7635633	0.89[EUR][1000 genomes]
rs7635871	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv869848	chr3:99652246-99904276	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99640400-99656000	Weak transcription	GM12878-XiMat	blood
2	chr3:99640400-99656600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr3:99640400-99656800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr3:99641400-99654200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr3:99644800-99663200	Weak transcription	Esophagus	oesophagus
6	chr3:99645200-99654200	Weak transcription	Small Intestine	intestine
7	chr3:99645200-99656800	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr3:99646000-99656400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr3:99648600-99656400	Weak transcription	Fetal Brain Male	brain
10	chr3:99648800-99654200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr3:99648800-99656800	Weak transcription	Fetal Heart	heart
12	chr3:99648800-99656800	Weak transcription	Psoas Muscle	Psoas
13	chr3:99648800-99663200	Weak transcription	Gastric	stomach
14	chr3:99648800-99664000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:99649000-99656200	Weak transcription	NH-A	brain
16	chr3:99649400-99654200	Weak transcription	Brain Anterior Caudate	brain
17	chr3:99649400-99656200	Weak transcription	HSMM	muscle
18	chr3:99649400-99656400	Weak transcription	Brain Angular Gyrus	brain
19	chr3:99649600-99654200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:99649600-99654200	Weak transcription	Stomach Mucosa	stomach
21	chr3:99649600-99656200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr3:99649600-99662800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr3:99649800-99654200	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr3:99649800-99654200	Weak transcription	Aorta	Aorta
25	chr3:99649800-99654200	Weak transcription	Fetal Muscle Leg	muscle
26	chr3:99649800-99654200	Weak transcription	Left Ventricle	heart
27	chr3:99649800-99654200	Weak transcription	Right Atrium	heart
28	chr3:99649800-99654200	Weak transcription	Right Ventricle	heart
29	chr3:99650000-99654200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr3:99650000-99654200	Weak transcription	Fetal Stomach	stomach
31	chr3:99650200-99656800	Weak transcription	Primary hematopoietic stem cells	blood
32	chr3:99650400-99663000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr3:99650400-99667400	Weak transcription	A549	lung
34	chr3:99650600-99654200	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr3:99650600-99656200	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr3:99650600-99662800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr3:99650600-99663200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr3:99651800-99656800	Weak transcription	Primary B cells from cord blood	blood
39	chr3:99652400-99656800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr3:99652600-99654800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr3:99652800-99655200	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr3:99653000-99654600	Enhancers	HUVEC	blood vessel
43	chr3:99653000-99654800	Enhancers	Placenta Amnion	Placenta Amnion
44	chr3:99653400-99654200	Enhancers	Colon Smooth Muscle	Colon
45	chr3:99653400-99654400	Enhancers	Brain Germinal Matrix	brain
46	chr3:99653400-99654600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr3:99653400-99654600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr3:99653400-99654600	Enhancers	Fetal Intestine Large	intestine
49	chr3:99653400-99654600	Enhancers	Stomach Smooth Muscle	stomach
50	chr3:99653400-99654800	Enhancers	HMEC	breast

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