Variant report

Variant	rs2878438
Chromosome Location	chr3:52103045-52103046
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:52086312..52088245-chr3:52101960..52104094,2	MCF-7	breast:
2	chr3:52088850..52094059-chr3:52101784..52106262,6	MCF-7	breast:
3	chr3:52102072..52104236-chr3:52134080..52136979,2	K562	blood:
4	chr3:52101388..52103446-chr3:52108588..52110470,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164086	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs12495536	0.88[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12496447	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12629791	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13316105	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2334961	1.00[CEU][hapmap];0.82[YRI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28387060	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34162321	0.81[ASN][1000 genomes]
rs352152	0.93[CEU][hapmap];0.97[GIH][hapmap];0.83[MEX][hapmap];0.96[TSI][hapmap];0.86[EUR][1000 genomes]
rs4687607	0.94[ASW][hapmap];0.93[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4687609	0.83[MEX][hapmap]
rs4687805	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4687810	0.94[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6773704	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6777340	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6778442	0.87[ASW][hapmap];0.93[CEU][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6786592	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs731684	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs735768	0.94[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs747343	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs749995	0.94[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7616695	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7644325	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs876782	0.86[YRI][hapmap];0.81[AFR][1000 genomes]
rs893055	0.88[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.80[LWK][hapmap];0.96[MEX][hapmap];0.90[TSI][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9809254	0.86[YRI][hapmap];0.81[AFR][1000 genomes]
rs9828327	1.00[CEU][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9846049	0.80[YRI][hapmap]
rs9848727	0.81[AMR][1000 genomes]
rs9851576	0.94[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9866081	0.82[AMR][1000 genomes]
rs9874939	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520211	chr3:51772347-52166147	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv1804090	chr3:51962081-52140591	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	esv1835339	chr3:51962081-52140591	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
4	nsv1003581	chr3:51973395-52108645	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
5	nsv1001062	chr3:51973395-52134638	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
6	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
7	nsv876786	chr3:52041566-52236762	Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
8	nsv984541	chr3:52055970-52285682	Genic enhancers Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52091800-52106000	Enhancers	Esophagus	oesophagus
2	chr3:52092000-52106400	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr3:52092200-52104200	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr3:52092200-52104800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr3:52092200-52107800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:52092600-52104800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr3:52096000-52107800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:52096400-52106400	Weak transcription	Fetal Thymus	thymus
9	chr3:52096800-52104000	Weak transcription	Stomach Smooth Muscle	stomach
10	chr3:52097000-52103600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr3:52097000-52105000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr3:52097000-52105000	Weak transcription	Hela-S3	cervix
13	chr3:52097200-52103400	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr3:52097200-52104000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr3:52097400-52104000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr3:52097400-52105400	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr3:52097400-52110800	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr3:52097600-52103400	Weak transcription	Brain Substantia Nigra	brain
19	chr3:52097600-52108200	Weak transcription	NHLF	lung
20	chr3:52097600-52119800	Weak transcription	GM12878-XiMat	blood
21	chr3:52098800-52106400	Enhancers	Fetal Muscle Leg	muscle
22	chr3:52099400-52107000	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr3:52099800-52104600	Weak transcription	HUVEC	blood vessel
24	chr3:52100000-52103800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr3:52100000-52104000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr3:52100000-52104000	Weak transcription	Pancreas	Pancrea
27	chr3:52100000-52104200	Weak transcription	Right Atrium	heart
28	chr3:52100000-52108200	Weak transcription	Gastric	stomach
29	chr3:52100200-52103400	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr3:52100200-52103600	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr3:52100200-52106600	Enhancers	Fetal Muscle Trunk	muscle
32	chr3:52100600-52103200	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr3:52100600-52103800	Weak transcription	Lung	lung
34	chr3:52100600-52105600	Weak transcription	Dnd41	blood
35	chr3:52100800-52104200	Weak transcription	Left Ventricle	heart
36	chr3:52101200-52104000	Weak transcription	Right Ventricle	heart
37	chr3:52101200-52105800	Enhancers	Placenta	Placenta
38	chr3:52101400-52103400	Enhancers	Fetal Intestine Large	intestine
39	chr3:52101400-52103800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr3:52101800-52110200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr3:52102000-52103200	Enhancers	Spleen	Spleen
42	chr3:52102000-52103600	Enhancers	Fetal Intestine Small	intestine
43	chr3:52102000-52104600	Weak transcription	NHEK	skin
44	chr3:52102000-52111200	Weak transcription	Fetal Kidney	kidney
45	chr3:52102200-52104600	Weak transcription	HMEC	breast
46	chr3:52102200-52105600	Enhancers	Fetal Stomach	stomach
47	chr3:52102200-52107600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr3:52102400-52103400	Enhancers	HepG2	liver
49	chr3:52102400-52104200	Weak transcription	NHDF-Ad	bronchial
50	chr3:52102400-52104600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links