Variant report

Variant	rs3797498
Chromosome Location	chr5:52333939-52333940
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:52326404..52328383-chr5:52333260..52335027,2	MCF-7	breast:
2	chr5:52285122..52287993-chr5:52333837..52337640,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000249899	Chromatin interaction
ENSG00000164171	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10940290	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1126643	0.91[YRI][hapmap]
rs11959632	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12521915	0.83[CEU][hapmap];0.87[YRI][hapmap]
rs12652168	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12657429	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12657501	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12657972	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12657980	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1316250	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1363192	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1421937	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1445943	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16880669	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1862191	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2303122	0.83[CEU][hapmap]
rs3212424	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3212438	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212439	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212441	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212450	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212453	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3212455	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212457	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212458	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3212461	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212464	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212467	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs3212472	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs3212478	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212480	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212481	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212486	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756537	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3776787	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3797495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3797496	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3822558	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3926397	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62357232	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62357233	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67719154	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs6880055	0.83[CEU][hapmap];0.93[CHB][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7725246	0.87[YRI][hapmap]
rs989073	0.86[AFR][1000 genomes];0.84[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	nsv471013	chr5:51779197-52339114	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv949005	chr5:52188028-52808229	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv830296	chr5:52209528-52410253	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv880425	chr5:52291279-52345868	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv881652	chr5:52323568-52385312	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv880389	chr5:52333420-52375199	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52314200-52348000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr5:52324200-52334200	Weak transcription	Spleen	Spleen
3	chr5:52324400-52356400	Weak transcription	Brain Anterior Caudate	brain
4	chr5:52327800-52334400	Weak transcription	Pancreas	Pancrea
5	chr5:52327800-52344200	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr5:52328000-52369200	Weak transcription	Fetal Intestine Small	intestine
7	chr5:52328600-52335200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr5:52328800-52335800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr5:52328800-52348000	Weak transcription	Fetal Intestine Large	intestine
10	chr5:52329000-52334200	Weak transcription	Lung	lung
11	chr5:52329400-52335600	Weak transcription	Dnd41	blood
12	chr5:52331000-52336200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr5:52331000-52337000	Weak transcription	Fetal Kidney	kidney
14	chr5:52331800-52334400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr5:52331800-52334800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr5:52331800-52334800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr5:52331800-52335200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr5:52331800-52337200	Enhancers	HUVEC	blood vessel
19	chr5:52332000-52334200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr5:52332000-52334400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr5:52332000-52334600	Enhancers	NH-A	brain
22	chr5:52332000-52334600	Enhancers	Osteobl	bone
23	chr5:52332000-52334800	Enhancers	Brain Hippocampus Middle	brain
24	chr5:52332200-52334000	Enhancers	Small Intestine	intestine
25	chr5:52332400-52334200	Weak transcription	Right Atrium	heart
26	chr5:52332400-52334600	Enhancers	Muscle Satellite Cultured Cells	--
27	chr5:52332800-52334200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr5:52332800-52334200	Weak transcription	Esophagus	oesophagus
29	chr5:52332800-52334800	Enhancers	Stomach Mucosa	stomach
30	chr5:52333000-52334000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr5:52333000-52334000	Enhancers	HSMM	muscle
32	chr5:52333000-52334400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr5:52333000-52334800	Enhancers	Brain Substantia Nigra	brain
34	chr5:52333200-52334000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr5:52333200-52334200	Enhancers	HSMMtube	muscle
36	chr5:52333200-52334400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr5:52333200-52334600	Enhancers	Adipose Nuclei	Adipose
38	chr5:52333400-52334200	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr5:52333400-52334600	Transcr. at gene 5' and 3'	NHEK	skin
40	chr5:52333400-52337000	Weak transcription	Duodenum Mucosa	Duodenum
41	chr5:52333400-52341400	Strong transcription	HepG2	liver
42	chr5:52333600-52334400	Flanking Active TSS	HMEC	breast
43	chr5:52333600-52334600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr5:52333600-52334600	Enhancers	Right Ventricle	heart
45	chr5:52333600-52334600	Enhancers	Skeletal Muscle Female	skeletal muscle
46	chr5:52333600-52336800	Weak transcription	Fetal Lung	lung
47	chr5:52333800-52334000	Flanking Active TSS	NHLF	lung
48	chr5:52333800-52334400	Enhancers	Placenta	Placenta
49	chr5:52333800-52334400	Enhancers	Sigmoid Colon	Sigmoid Colon
50	chr5:52333800-52334600	Enhancers	Brain Cingulate Gyrus	brain

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