Variant report

Variant	rs11904144
Chromosome Location	chr2:127880106-127880107
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs11682186	0.89[EUR][1000 genomes]
rs11691237	0.86[CEU][hapmap]
rs11693422	0.81[CEU][hapmap]
rs11694264	0.88[EUR][1000 genomes]
rs4663095	0.84[EUR][1000 genomes]
rs55654668	0.89[EUR][1000 genomes]
rs56117224	0.88[EUR][1000 genomes]
rs6751498	0.81[ASW][hapmap];0.81[GIH][hapmap];0.80[MKK][hapmap];0.94[YRI][hapmap]
rs749007	0.89[EUR][1000 genomes]
rs7575579	0.81[ASW][hapmap];0.81[GIH][hapmap];0.80[MKK][hapmap];0.94[YRI][hapmap]
rs9653202	0.81[ASW][hapmap];0.81[GIH][hapmap];0.80[MKK][hapmap];0.94[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	nsv999422	chr2:127464647-127956543	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv1004930	chr2:127477369-127938234	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv875012	chr2:127800981-127895573	Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	nsv1005149	chr2:127841930-127880106	Bivalent Enhancer ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	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
9	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
10	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
11	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
12	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11904144	BIN1	cis	lymphoblastoid	seeQTL
rs11904144	BIN1	cis	Whole Blood	GTEx
rs11904144	BIN1	Cis_1M	lymphoblastoid	RTeQTL
rs11904144	BIN1	cis	multi-tissue	Pritchard

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:127870600-127898400	Weak transcription	Right Atrium	heart
2	chr2:127873400-127886000	Weak transcription	Spleen	Spleen
3	chr2:127874000-127886000	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr2:127874200-127881200	Weak transcription	Fetal Intestine Small	intestine
5	chr2:127876000-127883400	Weak transcription	Brain Substantia Nigra	brain
6	chr2:127876000-127885800	Weak transcription	Brain Angular Gyrus	brain
7	chr2:127878200-127880400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr2:127878200-127880600	Enhancers	Fetal Muscle Trunk	muscle
9	chr2:127878200-127881000	Enhancers	Fetal Muscle Leg	muscle
10	chr2:127878400-127880400	Enhancers	Brain Inferior Temporal Lobe	brain
11	chr2:127878600-127880200	Enhancers	NHDF-Ad	bronchial
12	chr2:127878800-127880400	Enhancers	Brain Anterior Caudate	brain
13	chr2:127879000-127880200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr2:127879000-127880400	Enhancers	Brain Hippocampus Middle	brain
15	chr2:127879400-127880200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr2:127879600-127881000	Weak transcription	Fetal Intestine Large	intestine
17	chr2:127879600-127884400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr2:127879800-127883000	Weak transcription	Brain Cingulate Gyrus	brain
19	chr2:127880000-127880200	Enhancers	Skeletal Muscle Male	skeletal muscle

Quick Search:

Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

what's new

Quick links