Variant report

Variant	rs7648978
Chromosome Location	chr3:155499906-155499907
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	chr3:155489353..155491545-chr3:155498387..155500105,2	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs17349490	0.84[AMR][1000 genomes]
rs17349560	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17415195	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17415343	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56213840	1.00[ASN][1000 genomes]
rs57149264	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58227176	1.00[ASN][1000 genomes]
rs6765861	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6782387	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73156584	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73156593	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73156598	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73156600	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73156602	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73159011	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73159017	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73159021	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73159025	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73159026	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73159032	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73159054	1.00[ASN][1000 genomes]
rs73159063	1.00[ASN][1000 genomes]
rs73159074	1.00[ASN][1000 genomes]
rs73159092	1.00[ASN][1000 genomes]
rs73873405	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7615287	1.00[ASN][1000 genomes]
rs7615938	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7617878	1.00[ASN][1000 genomes]
rs7621415	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7641701	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9757945	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9882341	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877680	chr3:155438022-155723064	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1009635	chr3:155475438-155515484	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1007915	chr3:155476547-155513397	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv592080	chr3:155479222-155511844	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	esv14416	chr3:155479247-155512774	ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv592082	chr3:155481097-155500859	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv1006439	chr3:155481097-155515484	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	nsv1014031	chr3:155481097-155524777	Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
9	nsv999641	chr3:155481097-155534616	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
10	nsv1001756	chr3:155487190-155515484	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
11	esv2753744	chr3:155487298-155707298	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:155463800-155501200	Weak transcription	Aorta	Aorta
2	chr3:155467200-155500200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr3:155467200-155508000	Weak transcription	K562	blood
4	chr3:155467200-155508800	Weak transcription	Hela-S3	cervix
5	chr3:155467400-155508400	Weak transcription	HepG2	liver
6	chr3:155471400-155509000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr3:155472800-155500000	Weak transcription	Brain Cingulate Gyrus	brain
8	chr3:155476600-155500000	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr3:155478600-155509000	Weak transcription	Gastric	stomach
10	chr3:155480200-155509200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr3:155480400-155500200	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr3:155480600-155503800	Weak transcription	HUVEC	blood vessel
13	chr3:155487000-155510600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr3:155487000-155511400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr3:155487600-155524200	Weak transcription	Fetal Heart	heart
16	chr3:155488200-155500200	Weak transcription	Brain Angular Gyrus	brain
17	chr3:155488200-155500400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr3:155488200-155508600	Weak transcription	Lung	lung
19	chr3:155488200-155508600	Weak transcription	A549	lung
20	chr3:155488200-155508800	Weak transcription	Esophagus	oesophagus
21	chr3:155488200-155509400	Weak transcription	Left Ventricle	heart
22	chr3:155488200-155523200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr3:155488800-155508600	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr3:155489000-155523200	Weak transcription	Thymus	Thymus
25	chr3:155489400-155500200	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr3:155489800-155509600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr3:155490000-155509000	Weak transcription	Pancreas	Pancrea
28	chr3:155490400-155500000	Weak transcription	Brain Anterior Caudate	brain
29	chr3:155490800-155500000	Weak transcription	Dnd41	blood
30	chr3:155490800-155509600	Weak transcription	Psoas Muscle	Psoas
31	chr3:155491000-155500000	Weak transcription	Colon Smooth Muscle	Colon
32	chr3:155491600-155508800	Weak transcription	Stomach Smooth Muscle	stomach
33	chr3:155491600-155523200	Weak transcription	Rectal Smooth Muscle	rectum
34	chr3:155492400-155500800	Weak transcription	HSMMtube	muscle
35	chr3:155493000-155500000	Weak transcription	Adipose Nuclei	Adipose
36	chr3:155493000-155508800	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr3:155493200-155508800	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr3:155494400-155523600	Weak transcription	Small Intestine	intestine
39	chr3:155495000-155508400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr3:155496600-155508600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr3:155497000-155500000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr3:155497000-155500000	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr3:155497000-155501400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr3:155497400-155502400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr3:155497800-155502400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr3:155498600-155500200	Weak transcription	Fetal Muscle Trunk	muscle
47	chr3:155498600-155509000	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr3:155498800-155500000	Weak transcription	Primary T cells from cord blood	blood
49	chr3:155498800-155500000	Weak transcription	Primary hematopoietic stem cells	blood
50	chr3:155498800-155508800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links