Variant report

Variant	rs40020
Chromosome Location	chr5:16804121-16804122
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:16803623..16804217-chr5:16933825..16934788,2	MCF-7	breast:
2	chr5:16803694..16804550-chr5:17190688..17191667,2	MCF-7	breast:
3	chr5:16803642..16805897-chr5:16806344..16809776,4	MCF-7	breast:

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12188617	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs153409	0.81[CEU][hapmap]
rs250353	0.89[CEU][hapmap]
rs250356	0.92[CEU][hapmap];0.81[AMR][1000 genomes]
rs253359	0.85[CEU][hapmap]
rs253363	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs253365	0.96[CEU][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs253366	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs253367	0.96[CEU][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs253370	0.83[EUR][1000 genomes]
rs28297	0.87[ASW][hapmap];0.96[CEU][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.86[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs33401	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs33402	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs33405	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs385552	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs451009	0.82[EUR][1000 genomes]
rs496033	0.96[CEU][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs890825	0.83[TSI][hapmap]

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	nsv1025225	chr5:16714512-17234866	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	esv3529928	chr5:16748426-16856563	Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
3	esv3529929	chr5:16748426-16856563	Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv1030550	chr5:16748966-16872084	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv1015247	chr5:16748966-17133274	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv597309	chr5:16791857-16837862	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region miRNA target site	n/a	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:16764600-16807400	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr5:16783400-16810000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr5:16784600-16809200	Weak transcription	Ovary	ovary
4	chr5:16785800-16804200	Weak transcription	HSMM	muscle
5	chr5:16789400-16809200	Weak transcription	NHLF	lung
6	chr5:16791800-16807000	Weak transcription	Fetal Kidney	kidney
7	chr5:16791800-16807400	Weak transcription	Psoas Muscle	Psoas
8	chr5:16793000-16807600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr5:16793200-16805400	Weak transcription	Fetal Muscle Trunk	muscle
10	chr5:16793400-16807600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr5:16795000-16806800	Weak transcription	Fetal Stomach	stomach
12	chr5:16795000-16807000	Weak transcription	Fetal Lung	lung
13	chr5:16795000-16807400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr5:16795000-16807400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr5:16795200-16806800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr5:16795200-16829800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr5:16797000-16804200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr5:16797000-16809200	Weak transcription	NH-A	brain
19	chr5:16797200-16806800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr5:16797400-16809800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr5:16797400-16817400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr5:16798400-16809200	Weak transcription	NHEK	skin
23	chr5:16798600-16807600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr5:16798800-16807400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr5:16799000-16812200	Weak transcription	Fetal Intestine Small	intestine
26	chr5:16800400-16804400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr5:16800400-16805400	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr5:16800800-16808000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr5:16801000-16807800	Weak transcription	HUVEC	blood vessel
30	chr5:16801000-16809200	Weak transcription	Osteobl	bone
31	chr5:16801000-16809400	Weak transcription	Spleen	Spleen
32	chr5:16802200-16806600	Weak transcription	Fetal Brain Male	brain
33	chr5:16802200-16811400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr5:16803800-16804800	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr5:16803800-16805200	Enhancers	A549	lung
36	chr5:16804000-16804400	Enhancers	Lung	lung
37	chr5:16804000-16804600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr5:16804000-16804600	Enhancers	Gastric	stomach
39	chr5:16804000-16804600	Enhancers	Pancreas	Pancrea
40	chr5:16804000-16804800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr5:16804000-16805200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr5:16804000-16805800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links