Variant report

Variant	rs4663097
Chromosome Location	chr2:127861906-127861907
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	chr2:127853140..127855394-chr2:127860485..127862176,2	MCF-7	breast:
2	chr2:127857696..127862567-chr2:127862895..127866178,8	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CYP27C1-1	chr2:127861773-127862104	expReg_chr2_9105_-

Variant related genes	Relation type
ENSG00000136717	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs12989701	0.89[EUR][1000 genomes]
rs12994284	0.93[EUR][1000 genomes]
rs12994718	0.93[EUR][1000 genomes]
rs13004848	0.89[EUR][1000 genomes]
rs13009551	0.89[EUR][1000 genomes]
rs13029812	0.92[EUR][1000 genomes]
rs28434131	0.96[EUR][1000 genomes]
rs34608578	0.82[EUR][1000 genomes]
rs34745987	0.93[EUR][1000 genomes]
rs34854727	0.96[EUR][1000 genomes]
rs35832505	0.94[EUR][1000 genomes]
rs35860453	0.94[EUR][1000 genomes]
rs36085158	0.94[EUR][1000 genomes]
rs4663096	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6710467	0.91[EUR][1000 genomes]
rs6720234	0.93[EUR][1000 genomes]
rs71414738	0.93[EUR][1000 genomes]
rs7557280	0.94[EUR][1000 genomes]
rs7583814	0.92[EUR][1000 genomes]
rs873270	1.00[CEU][hapmap];0.95[TSI][hapmap];0.97[EUR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4663097	BIN1	cis	multi-tissue	Pritchard

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:127853200-127862000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr2:127853200-127862200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr2:127853200-127862400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr2:127853200-127862600	Weak transcription	NHLF	lung
5	chr2:127853200-127863000	Weak transcription	Primary hematopoietic stem cells	blood
6	chr2:127853400-127862400	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr2:127853600-127862200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr2:127854200-127862400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr2:127854800-127862400	Weak transcription	Right Atrium	heart
10	chr2:127856600-127862200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:127856800-127862200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr2:127857400-127862600	Genic enhancers	Fetal Intestine Small	intestine
13	chr2:127857600-127862600	Enhancers	Fetal Intestine Large	intestine
14	chr2:127857600-127863000	Enhancers	Gastric	stomach
15	chr2:127857800-127862800	Enhancers	Rectal Mucosa Donor 31	rectum
16	chr2:127857800-127863000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
17	chr2:127858000-127863600	Enhancers	Spleen	Spleen
18	chr2:127858200-127863000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr2:127858400-127863200	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr2:127858600-127862200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr2:127858600-127862400	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr2:127858800-127862600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr2:127858800-127862600	Enhancers	Rectal Mucosa Donor 29	rectum
24	chr2:127858800-127863600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr2:127859000-127862400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr2:127859000-127862600	Weak transcription	NH-A	brain
27	chr2:127859200-127862000	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr2:127859200-127862000	Weak transcription	Fetal Kidney	kidney
29	chr2:127859200-127862200	Weak transcription	Osteobl	bone
30	chr2:127859600-127862200	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr2:127859800-127862400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr2:127859800-127862400	Transcr. at gene 5' and 3'	Brain Cingulate Gyrus	brain
33	chr2:127859800-127862800	Flanking Active TSS	Brain Substantia Nigra	brain
34	chr2:127860000-127862400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr2:127860200-127862200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr2:127860200-127862200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr2:127860200-127862200	Weak transcription	A549	lung
38	chr2:127860200-127862600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr2:127860200-127862800	Enhancers	Lung	lung
40	chr2:127860600-127862000	Flanking Active TSS	HSMM	muscle
41	chr2:127860600-127862200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
42	chr2:127860600-127862400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr2:127860600-127863000	Enhancers	Esophagus	oesophagus
44	chr2:127860800-127862000	Flanking Active TSS	Fetal Muscle Trunk	muscle
45	chr2:127860800-127862400	Enhancers	Colon Smooth Muscle	Colon
46	chr2:127860800-127862600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr2:127860800-127862600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr2:127860800-127862600	Genic enhancers	Fetal Lung	lung
49	chr2:127860800-127862800	Enhancers	Fetal Stomach	stomach
50	chr2:127860800-127863000	Enhancers	H1 Cell Line	embryonic stem cell

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