Variant report

Variant	rs12139312
Chromosome Location	chr1:171225209-171225210
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:171223210..171225976-chr1:171227419..171229692,2	MCF-7	breast:
2	chr1:171219827..171222241-chr1:171222983..171225833,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231424	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12141357	0.83[EUR][1000 genomes]
rs12142492	0.83[EUR][1000 genomes]
rs12144402	0.83[EUR][1000 genomes]
rs12145368	0.83[EUR][1000 genomes]
rs28360369	0.83[EUR][1000 genomes]
rs28384856	0.83[EUR][1000 genomes]
rs28384863	0.83[EUR][1000 genomes]

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	nsv1001228	chr1:170885787-171452579	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
2	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv1005902	chr1:171036690-171254916	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv535203	chr1:171036690-171254916	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
5	esv10193	chr1:171128845-171414611	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv831882	chr1:171166224-171326083	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171221000-171226000	Weak transcription	Fetal Kidney	kidney
2	chr1:171221000-171226600	Weak transcription	Esophagus	oesophagus
3	chr1:171221000-171227600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr1:171221200-171226000	Weak transcription	Liver	Liver
5	chr1:171221200-171226000	Weak transcription	Fetal Lung	lung
6	chr1:171221200-171226400	Weak transcription	Right Atrium	heart
7	chr1:171221200-171227200	Enhancers	Fetal Intestine Small	intestine
8	chr1:171221200-171228200	Enhancers	Fetal Intestine Large	intestine
9	chr1:171221400-171226200	Weak transcription	Fetal Heart	heart
10	chr1:171221800-171226400	Weak transcription	Pancreas	Pancrea
11	chr1:171221800-171226800	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr1:171221800-171226800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr1:171222000-171226200	Weak transcription	Fetal Muscle Trunk	muscle
14	chr1:171222000-171226400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr1:171222000-171226600	Weak transcription	Placenta	Placenta
16	chr1:171222000-171227200	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr1:171222000-171227400	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr1:171223600-171226000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr1:171224400-171227200	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr1:171224600-171226400	Weak transcription	Gastric	stomach
21	chr1:171224800-171226600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr1:171224800-171227400	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr1:171224800-171227800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr1:171225000-171226000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr1:171225000-171226000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr1:171225000-171226000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr1:171225000-171226000	Weak transcription	Duodenum Mucosa	Duodenum
28	chr1:171225000-171226000	Weak transcription	HMEC	breast
29	chr1:171225000-171226000	Weak transcription	NHEK	skin
30	chr1:171225000-171226200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr1:171225000-171226400	Weak transcription	Small Intestine	intestine
32	chr1:171225000-171226400	Weak transcription	NHDF-Ad	bronchial
33	chr1:171225000-171227200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr1:171225000-171227600	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr1:171225000-171228000	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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