Variant report

Variant	rs3768865
Chromosome Location	chr2:127807019-127807020
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:127805679..127808550-chr2:127820998..127823785,2	MCF-7	breast:
2	chr2:127782007..127782956-chr2:127806151..127807307,3	MCF-7	breast:
3	chr2:127800876..127803938-chr2:127806149..127808710,3	MCF-7	breast:
4	chr2:127806982..127809850-chr2:127810680..127814139,4	K562	blood:

Variant related genes	Relation type
ENSG00000136717	Chromatin interaction
ENSG00000260163	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12476995	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12611852	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1438150	0.81[EUR][1000 genomes]
rs1438151	0.81[EUR][1000 genomes]
rs2071269	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2276582	0.90[ASN][1000 genomes]
rs2404176	0.83[EUR][1000 genomes]
rs3820759	0.90[ASN][1000 genomes]
rs4663088	0.81[EUR][1000 genomes]
rs56971880	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs59338031	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs66513437	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6713701	0.81[EUR][1000 genomes]
rs6728529	0.83[EUR][1000 genomes]
rs6736518	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs744887	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7571480	0.83[EUR][1000 genomes]
rs7572041	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7606043	0.90[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs893435	0.81[EUR][1000 genomes]
rs9636241	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 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	nsv459230	chr2:127771006-127844735	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv583032	chr2:127771006-127844735	Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1003730	chr2:127794288-127860830	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	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
7	nsv516759	chr2:127796666-127859441	Weak transcription Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
8	nsv1000994	chr2:127797089-127860830	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
9	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
10	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
11	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
12	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
13	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
14	nsv1002673	chr2:127801964-127860830	Enhancers Transcr. at gene 5' and 3' Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
15	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
16	nsv1011224	chr2:127802375-127860830	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
17	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
18	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
19	nsv1014290	chr2:127805366-127860830	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
20	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
21	nsv997855	chr2:127806424-127857946	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3768865	BIN1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:127783800-127815600	Weak transcription	Aorta	Aorta
2	chr2:127795800-127807600	Weak transcription	Brain Germinal Matrix	brain
3	chr2:127798200-127811400	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr2:127800000-127807600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr2:127800200-127807400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr2:127801600-127807600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr2:127802000-127818800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr2:127802200-127813600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr2:127802400-127816000	Weak transcription	Fetal Brain Male	brain
10	chr2:127802400-127822800	Weak transcription	Fetal Kidney	kidney
11	chr2:127803800-127807400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr2:127803800-127814200	Weak transcription	HSMM	muscle
13	chr2:127804000-127807600	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr2:127804000-127808000	Weak transcription	Right Ventricle	heart
15	chr2:127804000-127810600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr2:127804000-127813400	Weak transcription	Primary B cells from cord blood	blood
17	chr2:127804000-127814400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr2:127804200-127818200	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr2:127804200-127819600	Weak transcription	Osteobl	bone
20	chr2:127804400-127807200	Strong transcription	Brain Inferior Temporal Lobe	brain
21	chr2:127804400-127807200	Strong transcription	Fetal Stomach	stomach
22	chr2:127804400-127807400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr2:127804400-127807400	Strong transcription	Fetal Intestine Small	intestine
24	chr2:127804400-127820000	Genic enhancers	Fetal Muscle Trunk	muscle
25	chr2:127804600-127807200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr2:127804600-127807400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr2:127804600-127807400	Strong transcription	Spleen	Spleen
28	chr2:127804600-127807600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr2:127804600-127807600	Weak transcription	Pancreas	Pancrea
30	chr2:127804600-127810000	Strong transcription	Muscle Satellite Cultured Cells	--
31	chr2:127804600-127811400	Weak transcription	Duodenum Mucosa	Duodenum
32	chr2:127804600-127817400	Genic enhancers	Fetal Muscle Leg	muscle
33	chr2:127804600-127819200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr2:127804800-127807400	Strong transcription	Adipose Nuclei	Adipose
35	chr2:127804800-127808000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr2:127804800-127809200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr2:127804800-127809400	Genic enhancers	Skeletal Muscle Male	skeletal muscle
38	chr2:127804800-127818200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr2:127804800-127819400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr2:127805200-127807600	Strong transcription	Primary B cells from peripheral blood	blood
41	chr2:127805200-127807600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr2:127805200-127811200	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr2:127805400-127807200	Strong transcription	Brain Substantia Nigra	brain
44	chr2:127805400-127807400	Strong transcription	Primary T cells from cord blood	blood
45	chr2:127805400-127807400	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr2:127805400-127807400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr2:127805400-127807400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr2:127805400-127807800	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr2:127805400-127808000	Weak transcription	Esophagus	oesophagus
50	chr2:127805400-127808200	Strong transcription	HSMMtube	muscle

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