Variant report

Variant	rs55654668
Chromosome Location	chr2:127860880-127860881
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:127853140..127855394-chr2:127860485..127862176,2	MCF-7	breast:
2	chr2:127842254..127844330-chr2:127859021..127861716,3	MCF-7	breast:
3	chr2:127822004..127823991-chr2:127859645..127861835,2	MCF-7	breast:
4	chr2:127857696..127862567-chr2:127862895..127866178,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136717	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11554586	0.86[ASN][1000 genomes]
rs11682186	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11691237	0.84[EUR][1000 genomes]
rs11693422	0.82[EUR][1000 genomes]
rs11694264	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11904144	0.89[EUR][1000 genomes]
rs35114168	0.92[ASN][1000 genomes]
rs4663095	0.94[EUR][1000 genomes]
rs55646068	0.82[ASN][1000 genomes]
rs56026783	0.82[ASN][1000 genomes]
rs56117224	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56405130	1.00[ASN][1000 genomes]
rs72838215	1.00[ASN][1000 genomes]
rs749007	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 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	nsv1003461	chr2:127794288-127862257	Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	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
9	nsv1010577	chr2:127801964-127862257	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1003887	chr2:127802375-127862257	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv1009309	chr2:127802730-127862257	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv1010084	chr2:127805366-127862257	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv1001064	chr2:127828941-127862257	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	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
15	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
16	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
17	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
18	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
19	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
20	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs55654668	BIN1	Cis_1M	lymphoblastoid	RTeQTL
rs55654668	BIN1	cis	Whole Blood	GTEx

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:127853000-127861600	Weak transcription	NHDF-Ad	bronchial
2	chr2:127853200-127862000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr2:127853200-127862200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr2:127853200-127862400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr2:127853200-127862600	Weak transcription	NHLF	lung
6	chr2:127853200-127863000	Weak transcription	Primary hematopoietic stem cells	blood
7	chr2:127853400-127862400	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr2:127853600-127862200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr2:127854200-127862400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr2:127854800-127862400	Weak transcription	Right Atrium	heart
11	chr2:127856600-127861800	Weak transcription	Brain Germinal Matrix	brain
12	chr2:127856600-127862200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:127856800-127862200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr2:127857400-127862600	Genic enhancers	Fetal Intestine Small	intestine
15	chr2:127857600-127862600	Enhancers	Fetal Intestine Large	intestine
16	chr2:127857600-127863000	Enhancers	Gastric	stomach
17	chr2:127857800-127861400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr2:127857800-127862800	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr2:127857800-127863000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
20	chr2:127858000-127863600	Enhancers	Spleen	Spleen
21	chr2:127858200-127863000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr2:127858400-127861600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr2:127858400-127863200	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr2:127858600-127862200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr2:127858600-127862400	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr2:127858800-127862600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr2:127858800-127862600	Enhancers	Rectal Mucosa Donor 29	rectum
28	chr2:127858800-127863600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr2:127859000-127862400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr2:127859000-127862600	Weak transcription	NH-A	brain
31	chr2:127859200-127861000	Weak transcription	Pancreas	Pancrea
32	chr2:127859200-127861200	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr2:127859200-127862000	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr2:127859200-127862000	Weak transcription	Fetal Kidney	kidney
35	chr2:127859200-127862200	Weak transcription	Osteobl	bone
36	chr2:127859400-127861200	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
37	chr2:127859600-127861000	Transcr. at gene 5' and 3'	Brain Angular Gyrus	brain
38	chr2:127859600-127861000	Flanking Active TSS	HSMMtube	muscle
39	chr2:127859600-127861200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
40	chr2:127859600-127861800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr2:127859600-127862200	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr2:127859800-127861400	Weak transcription	Duodenum Mucosa	Duodenum
43	chr2:127859800-127862400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr2:127859800-127862400	Transcr. at gene 5' and 3'	Brain Cingulate Gyrus	brain
45	chr2:127859800-127862800	Flanking Active TSS	Brain Substantia Nigra	brain
46	chr2:127860000-127861000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr2:127860000-127861000	Transcr. at gene 5' and 3'	Brain Anterior Caudate	brain
48	chr2:127860000-127862400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr2:127860200-127861000	Weak transcription	Ovary	ovary
50	chr2:127860200-127861200	Weak transcription	Stomach Mucosa	stomach

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