Variant report

Variant	rs13414082
Chromosome Location	chr2:20345922-20345923
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:20342469..20346864-chr2:20382569..20386022,5	MCF-7	breast:
2	chr2:20343488..20346809-chr2:20347899..20350701,3	MCF-7	breast:
3	chr2:20344027..20347003-chr2:20348055..20350773,2	MCF-7	breast:
4	chr2:20313693..20315548-chr2:20343549..20346217,2	MCF-7	breast:
5	chr2:20343897..20346310-chr2:20367652..20370210,2	MCF-7	breast:
6	chr2:20343375..20346267-chr2:20420870..20424774,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115884	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10193851	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10205345	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13384258	0.82[CHB][hapmap]
rs13385323	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13386423	0.85[ASN][1000 genomes]
rs13389730	1.00[CHB][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs13398487	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13415910	0.82[CHB][hapmap]
rs16987384	0.80[ASN][1000 genomes]
rs16987387	1.00[CHB][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs28704637	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62109685	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6724651	0.83[ASN][1000 genomes]
rs7564193	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7586565	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7607854	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9306889	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009521	chr2:20310479-20388959	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	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
3	nsv1012055	chr2:20336237-20356606	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv1004083	chr2:20336237-20388138	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	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
6	nsv1004947	chr2:20342264-20388138	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv1005923	chr2:20344028-20369781	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20332200-20364400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:20334200-20346600	Enhancers	Placenta	Placenta
3	chr2:20336400-20346200	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr2:20338000-20346800	Enhancers	HMEC	breast
5	chr2:20339600-20349200	Weak transcription	Small Intestine	intestine
6	chr2:20339800-20348200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr2:20340000-20348000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr2:20340000-20348400	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr2:20340200-20348400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr2:20340800-20347200	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr2:20341800-20348600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr2:20341800-20348600	Weak transcription	Adipose Nuclei	Adipose
13	chr2:20341800-20348800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr2:20342000-20346200	Weak transcription	Osteobl	bone
15	chr2:20342000-20346400	Weak transcription	NHDF-Ad	bronchial
16	chr2:20342000-20348000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr2:20342000-20348200	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr2:20342000-20348400	Weak transcription	NHLF	lung
19	chr2:20342000-20348600	Weak transcription	Hela-S3	cervix
20	chr2:20342800-20347000	Enhancers	Stomach Mucosa	stomach
21	chr2:20343000-20346400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr2:20343400-20346200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr2:20343400-20348400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr2:20343600-20346000	Enhancers	Esophagus	oesophagus
25	chr2:20344000-20348200	Weak transcription	NH-A	brain
26	chr2:20344800-20346000	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr2:20344800-20346400	Enhancers	Placenta Amnion	Placenta Amnion
28	chr2:20345000-20346000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr2:20345000-20346000	Enhancers	Fetal Muscle Trunk	muscle
30	chr2:20345000-20346200	Enhancers	Duodenum Mucosa	Duodenum
31	chr2:20345000-20346800	Enhancers	Fetal Kidney	kidney
32	chr2:20345200-20346200	Bivalent Enhancer	HepG2	liver
33	chr2:20345200-20346400	Enhancers	Fetal Lung	lung
34	chr2:20345200-20346600	Enhancers	NHEK	skin
35	chr2:20345200-20348200	Weak transcription	HUVEC	blood vessel
36	chr2:20345400-20346200	Enhancers	Fetal Intestine Small	intestine
37	chr2:20345400-20346800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr2:20345600-20346000	Enhancers	ES-I3 Cell Line	embryonic stem cell
39	chr2:20345600-20346000	Enhancers	HUES6 Cell Line	embryonic stem cell
40	chr2:20345600-20346000	Enhancers	Fetal Intestine Large	intestine
41	chr2:20345600-20346200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr2:20345600-20346800	Flanking Active TSS	GM12878-XiMat	blood
43	chr2:20345600-20349800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr2:20345600-20356600	Weak transcription	Liver	Liver
45	chr2:20345800-20346000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr2:20345800-20346400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr2:20345800-20346400	Enhancers	K562	blood
48	chr2:20345800-20347800	Weak transcription	Lung	lung
49	chr2:20345800-20348000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr2:20345800-20348600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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