Variant report

Variant	rs73859911
Chromosome Location	chr3:99690439-99690440
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:99686155..99688649-chr3:99689841..99691929,2	MCF-7	breast:

Extended variants
information (count: 40 )
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	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	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	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73858966	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	0.87[AFR][1000 genomes];1.00[AMR][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:10 , 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
4	nsv932634	chr3:99660690-99888854	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1010579	chr3:99660754-99901817	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1008483	chr3:99660754-99903769	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1010897	chr3:99660754-99904783	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1001529	chr3:99661758-99892654	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
9	nsv536665	chr3:99661758-99892654	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
10	nsv999332	chr3:99690207-99774720	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99677400-99696600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr3:99677600-99692600	Weak transcription	Fetal Lung	lung
3	chr3:99678800-99691800	Enhancers	Skeletal Muscle Female	skeletal muscle
4	chr3:99679600-99697000	Weak transcription	Fetal Muscle Trunk	muscle
5	chr3:99685400-99691400	Weak transcription	Right Atrium	heart
6	chr3:99686400-99691200	Weak transcription	Fetal Stomach	stomach
7	chr3:99686400-99691400	Weak transcription	Colon Smooth Muscle	Colon
8	chr3:99686400-99691800	Weak transcription	Fetal Intestine Small	intestine
9	chr3:99686600-99691200	Weak transcription	Fetal Muscle Leg	muscle
10	chr3:99686600-99691200	Weak transcription	Stomach Smooth Muscle	stomach
11	chr3:99686600-99693400	Weak transcription	Placenta	Placenta
12	chr3:99687000-99691200	Weak transcription	HSMM	muscle
13	chr3:99687000-99691400	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr3:99687000-99691400	Weak transcription	Rectal Smooth Muscle	rectum
15	chr3:99687000-99693000	Weak transcription	Stomach Mucosa	stomach
16	chr3:99687200-99690600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr3:99687200-99695200	Weak transcription	Primary B cells from cord blood	blood
18	chr3:99688600-99694200	Weak transcription	Left Ventricle	heart
19	chr3:99689200-99693000	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr3:99689200-99697400	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr3:99689600-99690800	Enhancers	Sigmoid Colon	Sigmoid Colon
22	chr3:99689800-99690600	Enhancers	Psoas Muscle	Psoas
23	chr3:99689800-99702000	Weak transcription	Primary T cells from cord blood	blood
24	chr3:99690000-99692800	Weak transcription	GM12878-XiMat	blood
25	chr3:99690200-99690600	Enhancers	NHEK	skin
26	chr3:99690400-99690600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr3:99690400-99690600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr3:99690400-99690600	Enhancers	HMEC	breast
29	chr3:99690400-99690800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links