Variant report

Variant	rs11679418
Chromosome Location	chr2:127862472-127862473
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:127857696..127862567-chr2:127862895..127866178,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136717	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11675682	0.87[EUR][1000 genomes]
rs11693218	0.89[EUR][1000 genomes]
rs12617750	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13019394	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2164871	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3856378	0.89[EUR][1000 genomes]
rs4662705	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4663094	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6706041	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6708935	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6709337	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6709706	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6718147	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs730471	0.97[EUR][1000 genomes]
rs734115	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs754107	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs755639	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7560621	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	esv1825024	chr2:127798138-127864285	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv459241	chr2:127800981-127868435	Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv583033	chr2:127800981-127868435	Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv875011	chr2:127800981-127868435	Genic enhancers Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11679418	BIN1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:127853200-127862600	Weak transcription	NHLF	lung
2	chr2:127853200-127863000	Weak transcription	Primary hematopoietic stem cells	blood
3	chr2:127857400-127862600	Genic enhancers	Fetal Intestine Small	intestine
4	chr2:127857600-127862600	Enhancers	Fetal Intestine Large	intestine
5	chr2:127857600-127863000	Enhancers	Gastric	stomach
6	chr2:127857800-127862800	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr2:127857800-127863000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
8	chr2:127858000-127863600	Enhancers	Spleen	Spleen
9	chr2:127858200-127863000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr2:127858400-127863200	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr2:127858800-127862600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr2:127858800-127862600	Enhancers	Rectal Mucosa Donor 29	rectum
13	chr2:127858800-127863600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr2:127859000-127862600	Weak transcription	NH-A	brain
15	chr2:127859800-127862800	Flanking Active TSS	Brain Substantia Nigra	brain
16	chr2:127860200-127862600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr2:127860200-127862800	Enhancers	Lung	lung
18	chr2:127860600-127863000	Enhancers	Esophagus	oesophagus
19	chr2:127860800-127862600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr2:127860800-127862600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr2:127860800-127862600	Genic enhancers	Fetal Lung	lung
22	chr2:127860800-127862800	Enhancers	Fetal Stomach	stomach
23	chr2:127860800-127863000	Enhancers	H1 Cell Line	embryonic stem cell
24	chr2:127860800-127863000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
25	chr2:127860800-127863200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr2:127861000-127862600	Enhancers	Pancreas	Pancrea
27	chr2:127861000-127862800	Enhancers	Ovary	ovary
28	chr2:127861000-127863200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr2:127861000-127863200	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr2:127861200-127862600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr2:127861200-127862600	Enhancers	Duodenum Smooth Muscle	Duodenum
32	chr2:127861200-127863200	Enhancers	Stomach Mucosa	stomach
33	chr2:127861400-127862600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
34	chr2:127861400-127863000	Flanking Active TSS	Brain Anterior Caudate	brain
35	chr2:127861400-127863200	Enhancers	Duodenum Mucosa	Duodenum
36	chr2:127861400-127863400	Flanking Active TSS	Colonic Mucosa	Colon
37	chr2:127861600-127862600	Transcr. at gene 5' and 3'	Fetal Muscle Leg	muscle
38	chr2:127861600-127862800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
39	chr2:127861600-127863000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr2:127861600-127863000	Enhancers	Liver	Liver
41	chr2:127861800-127862600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr2:127861800-127862600	Active TSS	Hela-S3	cervix
43	chr2:127861800-127863000	Transcr. at gene 5' and 3'	Brain Hippocampus Middle	brain
44	chr2:127861800-127863200	Enhancers	Right Ventricle	heart
45	chr2:127861800-127864400	Flanking Active TSS	Adipose Nuclei	Adipose
46	chr2:127862000-127862600	Enhancers	HUES6 Cell Line	embryonic stem cell
47	chr2:127862000-127862600	Enhancers	Fetal Kidney	kidney
48	chr2:127862000-127862600	Transcr. at gene 5' and 3'	HSMM	muscle
49	chr2:127862000-127862600	Flanking Active TSS	HSMMtube	muscle
50	chr2:127862000-127862800	Transcr. at gene 5' and 3'	Fetal Muscle Trunk	muscle

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