Variant report

Variant	rs12299440
Chromosome Location	chr12:31003815-31003816
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:31003713..31004456-chr12:31138363..31139354,3	MCF-7	breast:

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12308573	0.91[ASN][1000 genomes]
rs12814038	0.82[EUR][1000 genomes]
rs1560017	0.82[EUR][1000 genomes]
rs34207804	0.82[EUR][1000 genomes]
rs4930939	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4931382	0.91[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.90[YRI][hapmap]
rs56377936	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61529138	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61916669	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61916685	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61917089	0.82[EUR][1000 genomes]
rs7306145	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949148	chr12:30800040-31131712	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	esv34091	chr12:30927650-31061815	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
3	nsv1052957	chr12:30951520-31191197	Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv541439	chr12:30951520-31191197	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv1052869	chr12:30951520-31399162	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	esv2422447	chr12:30954811-31449815	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	nsv832362	chr12:30957786-31124983	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv1053711	chr12:30959987-31156297	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv558030	chr12:30969675-31266287	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
10	esv3377311	chr12:30984179-31044167	Weak transcription Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:30986400-31006400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:31000800-31004000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr12:31000800-31004000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr12:31001000-31004200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr12:31002000-31004200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr12:31002400-31004400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr12:31003000-31004200	Enhancers	H9 Cell Line	embryonic stem cell
8	chr12:31003200-31004000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr12:31003200-31004200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr12:31003200-31004200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr12:31003200-31004200	Weak transcription	Esophagus	oesophagus
12	chr12:31003600-31004000	Enhancers	Primary B cells from peripheral blood	blood
13	chr12:31003600-31004000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr12:31003600-31004000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr12:31003600-31004000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr12:31003600-31004000	Enhancers	Fetal Intestine Large	intestine
17	chr12:31003600-31004200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr12:31003600-31004200	Bivalent Enhancer	Fetal Intestine Small	intestine
19	chr12:31003600-31004200	Enhancers	GM12878-XiMat	blood
20	chr12:31003600-31004600	Active TSS	Primary T helper cells PMA-I stimulated	--
21	chr12:31003800-31004000	Enhancers	Primary T cells fromperipheralblood	blood
22	chr12:31003800-31004000	Flanking Active TSS	Hela-S3	cervix
23	chr12:31003800-31004200	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr12:31003800-31004200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
25	chr12:31003800-31004200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr12:31003800-31004200	Enhancers	Dnd41	blood
27	chr12:31003800-31004200	Weak transcription	HepG2	liver
28	chr12:31003800-31004400	Enhancers	Lung	lung
29	chr12:31003800-31004800	Enhancers	H1 Cell Line	embryonic stem cell
30	chr12:31003800-31005000	Active TSS	Primary T regulatory cells fromperipheralblood	blood

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