Variant report

Variant	rs10205345
Chromosome Location	chr2:20344888-20344889
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:20342469..20346864-chr2:20382569..20386022,5	MCF-7	breast:
2	chr2:20337846..20345492-chr2:20421951..20427912,20	MCF-7	breast:
3	chr2:20343488..20346809-chr2:20347899..20350701,3	MCF-7	breast:
4	chr2:20344027..20347003-chr2:20348055..20350773,2	MCF-7	breast:
5	chr2:20313693..20315548-chr2:20343549..20346217,2	MCF-7	breast:
6	chr2:20343897..20346310-chr2:20367652..20370210,2	MCF-7	breast:
7	chr2:20343375..20346267-chr2:20420870..20424774,4	MCF-7	breast:
8	chr2:20338664..20345614-chr2:20377409..20381353,9	MCF-7	breast:

No data

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]
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];0.93[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13414082	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]
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];0.93[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:52 , 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	chr2:20338000-20345200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr2:20338000-20346800	Enhancers	HMEC	breast
6	chr2:20339600-20349200	Weak transcription	Small Intestine	intestine
7	chr2:20339800-20348200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr2:20340000-20345200	Weak transcription	Fetal Lung	lung
9	chr2:20340000-20348000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr2:20340000-20348400	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr2:20340200-20348400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr2:20340800-20347200	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr2:20341200-20345200	Weak transcription	Left Ventricle	heart
14	chr2:20341400-20345000	Weak transcription	Duodenum Mucosa	Duodenum
15	chr2:20341400-20345200	Weak transcription	HSMMtube	muscle
16	chr2:20341400-20345400	Weak transcription	Right Ventricle	heart
17	chr2:20341400-20345600	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr2:20341600-20345200	Weak transcription	K562	blood
19	chr2:20341600-20345600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:20341800-20345000	Weak transcription	Liver	Liver
21	chr2:20341800-20348600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr2:20341800-20348600	Weak transcription	Adipose Nuclei	Adipose
23	chr2:20341800-20348800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr2:20342000-20346200	Weak transcription	Osteobl	bone
25	chr2:20342000-20346400	Weak transcription	NHDF-Ad	bronchial
26	chr2:20342000-20348000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr2:20342000-20348200	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr2:20342000-20348400	Weak transcription	NHLF	lung
29	chr2:20342000-20348600	Weak transcription	Hela-S3	cervix
30	chr2:20342800-20347000	Enhancers	Stomach Mucosa	stomach
31	chr2:20343000-20345200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr2:20343000-20346400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr2:20343200-20345400	Weak transcription	Fetal Intestine Small	intestine
34	chr2:20343400-20345200	Weak transcription	NHEK	skin
35	chr2:20343400-20345400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr2:20343400-20345600	Weak transcription	Fetal Intestine Large	intestine
37	chr2:20343400-20346200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr2:20343400-20348400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr2:20343600-20346000	Enhancers	Esophagus	oesophagus
40	chr2:20344000-20345200	Weak transcription	A549	lung
41	chr2:20344000-20348200	Weak transcription	NH-A	brain
42	chr2:20344200-20345400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr2:20344200-20345800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr2:20344600-20345000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr2:20344600-20345200	Enhancers	HUVEC	blood vessel
46	chr2:20344600-20345600	Enhancers	GM12878-XiMat	blood
47	chr2:20344800-20345000	Weak transcription	Fetal Kidney	kidney
48	chr2:20344800-20345000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
49	chr2:20344800-20345800	Enhancers	Gastric	stomach
50	chr2:20344800-20345800	Enhancers	Spleen	Spleen

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