Variant report

Variant	rs4682825
Chromosome Location	chr3:46715001-46715002
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	chr3:46713668..46715350-chr3:46724195..46726906,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11711074	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12496585	0.89[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.85[EUR][1000 genomes]
rs3210183	1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34190208	0.83[EUR][1000 genomes]
rs3935248	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4076927	0.94[CHB][hapmap];0.87[JPT][hapmap]
rs55991232	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56069285	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61277784	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62246183	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6442020	0.94[CHB][hapmap];0.87[JPT][hapmap]
rs6792255	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7372799	0.94[CHB][hapmap];0.87[JPT][hapmap]
rs7373358	0.89[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap]
rs7426833	0.93[CHB][hapmap];0.87[JPT][hapmap]
rs7613489	0.94[CHB][hapmap];0.87[JPT][hapmap]
rs7625303	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7633016	0.94[CHB][hapmap];0.87[JPT][hapmap]
rs7634963	0.82[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap];0.84[EUR][1000 genomes]
rs7642448	0.94[CHB][hapmap];0.87[JPT][hapmap]
rs7642783	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs7649081	0.81[JPT][hapmap]
rs7650366	0.81[CHB][hapmap];0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007449	chr3:46652343-46986578	Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv536554	chr3:46652343-46986578	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv876739	chr3:46656980-46744966	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv876740	chr3:46656980-46748453	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv876741	chr3:46663372-46763839	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	nsv516623	chr3:46680063-46852679	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	esv2757869	chr3:46680452-46972489	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
8	esv2759147	chr3:46680452-46972489	Genic enhancers Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
9	esv1804680	chr3:46704348-46869911	Bivalent Enhancer Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	nsv876742	chr3:46705369-46763839	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
11	nsv536555	chr3:46706571-46817963	Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
12	nsv536556	chr3:46706571-46849443	Genic enhancers Bivalent/Poised TSS Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
13	nsv536557	chr3:46706571-46853434	Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
14	nsv536558	chr3:46706571-47024756	Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
15	nsv10268	chr3:46707169-46736718	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
16	esv1797503	chr3:46708712-46760713	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46702800-46732400	Weak transcription	Psoas Muscle	Psoas
2	chr3:46703000-46731600	Weak transcription	Hela-S3	cervix
3	chr3:46705400-46732600	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr3:46705400-46734400	Weak transcription	Ovary	ovary
5	chr3:46705800-46717000	Weak transcription	Brain Anterior Caudate	brain
6	chr3:46706000-46717400	Weak transcription	Brain Angular Gyrus	brain
7	chr3:46707200-46717000	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr3:46708000-46716600	Weak transcription	Stomach Smooth Muscle	stomach
9	chr3:46708000-46717200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr3:46710000-46722000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr3:46710200-46722800	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr3:46710400-46716800	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr3:46711200-46715200	Weak transcription	Duodenum Mucosa	Duodenum
14	chr3:46711400-46715800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr3:46711400-46716200	Strong transcription	Skeletal Muscle Male	skeletal muscle
16	chr3:46711400-46718400	Weak transcription	Right Atrium	heart
17	chr3:46711400-46726800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr3:46711400-46730400	Strong transcription	Primary T cells from cord blood	blood
19	chr3:46711400-46731800	Strong transcription	NHEK	skin
20	chr3:46711600-46717200	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr3:46711600-46731000	Strong transcription	Esophagus	oesophagus
22	chr3:46711800-46717400	Strong transcription	Placenta	Placenta
23	chr3:46711800-46731200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr3:46712000-46717600	Strong transcription	Spleen	Spleen
25	chr3:46712000-46720400	Strong transcription	Lung	lung
26	chr3:46712200-46717200	Strong transcription	Skeletal Muscle Female	skeletal muscle
27	chr3:46712400-46715800	Strong transcription	Gastric	stomach
28	chr3:46712400-46717200	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr3:46712400-46718600	Strong transcription	Sigmoid Colon	Sigmoid Colon
30	chr3:46712400-46730600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr3:46712600-46717400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr3:46712600-46718200	Strong transcription	Left Ventricle	heart
33	chr3:46712800-46715200	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr3:46713000-46717400	Strong transcription	Right Ventricle	heart
35	chr3:46713000-46732000	Weak transcription	Stomach Mucosa	stomach
36	chr3:46713400-46718200	Strong transcription	Colonic Mucosa	Colon
37	chr3:46713800-46716000	Genic enhancers	Fetal Intestine Small	intestine
38	chr3:46714600-46716000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr3:46714600-46716000	Strong transcription	Liver	Liver
40	chr3:46714800-46715200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr3:46714800-46715200	Enhancers	HUES6 Cell Line	embryonic stem cell
42	chr3:46714800-46715600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr3:46714800-46718000	Strong transcription	Adipose Nuclei	Adipose
44	chr3:46714800-46718000	Strong transcription	Aorta	Aorta
45	chr3:46714800-46729600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr3:46714800-46730400	Strong transcription	HMEC	breast
47	chr3:46715000-46715200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr3:46715000-46715600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
49	chr3:46715000-46715800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr3:46715000-46716200	Genic enhancers	Fetal Intestine Large	intestine

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