Variant report

Variant	rs3732162
Chromosome Location	chr2:20413750-20413751
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:20332825..20334861-chr2:20412416..20414197,2	MCF-7	breast:
2	chr2:20313389..20316167-chr2:20411646..20415090,3	MCF-7	breast:
3	chr2:20340564..20344464-chr2:20412010..20415688,4	MCF-7	breast:
4	chr2:20271585..20273476-chr2:20412468..20414471,2	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10175853	0.88[CEU][hapmap]
rs10192042	0.87[CEU][hapmap]
rs10495704	0.83[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs1106111	0.84[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs11096648	0.96[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11096649	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11096650	0.90[ASN][1000 genomes]
rs12373772	0.92[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12373819	0.92[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12464428	0.85[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs13415389	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2002090	0.84[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs2007340	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3732163	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3732164	0.83[CEU][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3755300	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3771227	0.81[ASN][1000 genomes]
rs3771229	0.90[ASN][1000 genomes]
rs3771232	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3771233	1.00[CEU][hapmap];0.92[CHB][hapmap];0.82[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3771236	0.85[CEU][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3771238	0.84[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3771239	0.84[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3771240	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3771241	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3771243	1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3771244	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3771246	0.96[ASN][1000 genomes]
rs3771247	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3821219	0.94[ASN][1000 genomes]
rs57938873	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59129757	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62109740	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62111433	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs72785203	0.90[ASN][1000 genomes]
rs72785204	0.90[ASN][1000 genomes]
rs72785206	0.90[ASN][1000 genomes]
rs7558833	0.87[CEU][hapmap]
rs7563245	0.92[CEU][hapmap];0.81[AMR][1000 genomes]
rs7585590	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9306890	0.88[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012841	chr2:20328894-20415168	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv1000323	chr2:20336237-20419923	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	esv1846803	chr2:20409322-20427189	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20391800-20423200	Weak transcription	Right Atrium	heart
2	chr2:20404000-20414000	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr2:20404000-20422400	Weak transcription	Brain Germinal Matrix	brain
4	chr2:20404600-20420800	Enhancers	Stomach Mucosa	stomach
5	chr2:20405000-20415000	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr2:20405200-20413800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr2:20405200-20414200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr2:20405200-20414600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr2:20405800-20416200	Enhancers	Gastric	stomach
10	chr2:20407800-20414800	Enhancers	Colonic Mucosa	Colon
11	chr2:20408600-20414800	Enhancers	Placenta	Placenta
12	chr2:20409400-20414400	Weak transcription	Small Intestine	intestine
13	chr2:20409400-20414800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr2:20409800-20414800	Weak transcription	Lung	lung
15	chr2:20410400-20416200	Genic enhancers	Fetal Intestine Small	intestine
16	chr2:20410600-20417400	Enhancers	Fetal Intestine Large	intestine
17	chr2:20410800-20414800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr2:20410800-20415200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr2:20410800-20415400	Enhancers	H1 Cell Line	embryonic stem cell
20	chr2:20411000-20415400	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr2:20411400-20414600	Enhancers	Fetal Thymus	thymus
22	chr2:20411400-20414800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr2:20411600-20413800	Enhancers	Fetal Stomach	stomach
24	chr2:20411600-20414200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr2:20411600-20414600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr2:20411600-20414800	Transcr. at gene 5' and 3'	NHEK	skin
27	chr2:20411800-20413800	Enhancers	Fetal Lung	lung
28	chr2:20411800-20414400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:20411800-20414800	Enhancers	Placenta Amnion	Placenta Amnion
30	chr2:20412000-20413800	Enhancers	Fetal Kidney	kidney
31	chr2:20412000-20414000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr2:20412000-20414400	Flanking Active TSS	HMEC	breast
33	chr2:20412000-20415000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr2:20412200-20414200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr2:20412400-20414200	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr2:20412400-20416000	Flanking Active TSS	HepG2	liver
37	chr2:20412600-20414800	Enhancers	HUES48 Cell Line	embryonic stem cell
38	chr2:20412600-20415400	Enhancers	A549	lung
39	chr2:20412600-20420600	Weak transcription	NHLF	lung
40	chr2:20412800-20413800	Flanking Active TSS	Duodenum Mucosa	Duodenum
41	chr2:20412800-20414000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr2:20412800-20414000	Flanking Active TSS	GM12878-XiMat	blood
43	chr2:20412800-20415000	Enhancers	iPS-20b Cell Line	embryonic stem cell
44	chr2:20412800-20416400	Enhancers	Rectal Mucosa Donor 29	rectum
45	chr2:20413000-20413800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr2:20413000-20414200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr2:20413000-20415000	Enhancers	iPS-18 Cell Line	embryonic stem cell
48	chr2:20413000-20415600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr2:20413000-20416200	Enhancers	Sigmoid Colon	Sigmoid Colon
50	chr2:20413000-20417600	Enhancers	Rectal Mucosa Donor 31	rectum

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