Variant report

Variant	rs11890243
Chromosome Location	chr2:127958041-127958042
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	chr2:127957550..127959520-chr2:127975505..127977152,2	MCF-7	breast:
2	chr2:127957491..127959213-chr2:128050119..128052916,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163161	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs11683344	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11683427	0.85[CHB][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006112	chr2:127830117-128032546	Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	esv2757832	chr2:127830943-128006514	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	esv2759090	chr2:127830943-128006514	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv1011378	chr2:127841930-128020546	Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv999809	chr2:127841930-128032546	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv1010669	chr2:127848860-128032546	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription 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 target site	8 gene(s)	inside rSNPs	diseases
7	nsv1003599	chr2:127871183-128059407	Strong transcription Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv535920	chr2:127871183-128059407	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11890243	ERCC3	cis	cerebellum	SCAN
rs11890243	ERCC3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:127934600-127965600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:127941000-127963000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:127943000-127959400	Weak transcription	Gastric	stomach
4	chr2:127948600-127959400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr2:127948800-127973400	Weak transcription	HMEC	breast
6	chr2:127951200-127965800	Weak transcription	Esophagus	oesophagus
7	chr2:127951400-127962200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr2:127951600-127958600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr2:127952000-127963000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr2:127952200-127959000	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr2:127952200-127964400	Weak transcription	Right Atrium	heart
12	chr2:127952200-127975200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr2:127952400-127958800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr2:127952400-127959200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr2:127953200-127958600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr2:127953600-127958200	Weak transcription	Fetal Muscle Leg	muscle
17	chr2:127953600-127961000	Strong transcription	Fetal Stomach	stomach
18	chr2:127954200-127964000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr2:127954600-127962800	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr2:127954800-127960000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr2:127954800-127965600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr2:127955000-127965600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr2:127955400-127958800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr2:127955400-127959200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr2:127955600-127961200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr2:127955600-127962800	Weak transcription	Brain Hippocampus Middle	brain
27	chr2:127955800-127963000	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr2:127956000-127961400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:127956200-127959400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr2:127956400-127975800	Weak transcription	Fetal Kidney	kidney
31	chr2:127957200-127958600	Weak transcription	Fetal Muscle Trunk	muscle
32	chr2:127957200-127962600	Weak transcription	Fetal Brain Female	brain
33	chr2:127957400-127962200	Weak transcription	Fetal Lung	lung
34	chr2:127957400-127965800	Weak transcription	NHEK	skin
35	chr2:127957800-127963200	Weak transcription	Fetal Intestine Small	intestine

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