Variant report

Variant	rs9953917
Chromosome Location	chr18:12289927-12289928
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:12284886..12287018-chr18:12289577..12291293,2	MCF-7	breast:
2	chr18:12282293..12284100-chr18:12288664..12290381,2	MCF-7	breast:
3	chr18:12289075..12291340-chr18:12294128..12296061,2	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11662978	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4797669	0.91[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6505747	1.00[YRI][hapmap]
rs7504499	0.84[AFR][1000 genomes]
rs7505123	1.00[YRI][hapmap]
rs7505582	0.98[AFR][1000 genomes]
rs7506533	0.95[AFR][1000 genomes]
rs7506586	1.00[YRI][hapmap]
rs8098341	0.84[AFR][1000 genomes]
rs9956239	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9960329	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063125	chr18:12046892-12918251	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
2	nsv491873	chr18:12159445-12739784	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
3	nsv909400	chr18:12201374-12585545	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	nsv909401	chr18:12211483-12312075	Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
5	nsv909402	chr18:12211483-12325222	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
6	nsv909403	chr18:12231060-12325222	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
7	nsv1061545	chr18:12235999-12328405	Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
8	esv2758471	chr18:12240681-12499525	Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
9	esv2758714	chr18:12240681-12499525	Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
10	nsv576496	chr18:12247872-12490502	Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
11	nsv870342	chr18:12270808-12295798	Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	nsv1058661	chr18:12280366-12313865	Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12288400-12296200	Weak transcription	Spleen	Spleen
2	chr18:12288600-12291800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr18:12288600-12291800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr18:12289000-12290200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr18:12289000-12290200	Weak transcription	Gastric	stomach
6	chr18:12289000-12290400	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
7	chr18:12289000-12290400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr18:12289000-12292600	Weak transcription	Aorta	Aorta
9	chr18:12289000-12304800	Weak transcription	Pancreas	Pancrea
10	chr18:12289200-12290000	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr18:12289200-12290000	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr18:12289200-12290000	Enhancers	Colon Smooth Muscle	Colon
13	chr18:12289200-12290000	Weak transcription	NHDF-Ad	bronchial
14	chr18:12289200-12290200	Bivalent Enhancer	HepG2	liver
15	chr18:12289200-12290400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr18:12289200-12290400	Enhancers	Placenta	Placenta
17	chr18:12289200-12290600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr18:12289200-12291800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr18:12289200-12291800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr18:12289200-12294000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr18:12289200-12306400	Weak transcription	Right Atrium	heart
22	chr18:12289400-12290000	Enhancers	K562	blood
23	chr18:12289400-12290200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr18:12289400-12290200	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr18:12289400-12290200	Enhancers	NHEK	skin
26	chr18:12289400-12290400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr18:12289400-12290400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr18:12289400-12290400	Enhancers	Adipose Nuclei	Adipose
29	chr18:12289400-12290400	Bivalent Enhancer	Fetal Muscle Leg	muscle
30	chr18:12289400-12290400	Enhancers	HMEC	breast
31	chr18:12289400-12290400	Enhancers	HSMM	muscle
32	chr18:12289400-12290600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
33	chr18:12289400-12295600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr18:12289400-12298200	Weak transcription	Fetal Heart	heart
35	chr18:12289400-12306400	Weak transcription	NHLF	lung
36	chr18:12289600-12290000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr18:12289600-12290000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr18:12289800-12290000	Enhancers	ES-I3 Cell Line	embryonic stem cell
39	chr18:12289800-12290000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
40	chr18:12289800-12290000	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
41	chr18:12289800-12290000	Flanking Active TSS	Stomach Smooth Muscle	stomach
42	chr18:12289800-12290400	Flanking Active TSS	HSMMtube	muscle

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