Variant report

Variant	rs4663088
Chromosome Location	chr2:127782322-127782323
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	YY1	chr2:127782199-127783533	H1-hESC	embryonic stem cell:	n/a	chr2:127783193-127783204 chr2:127782458-127782472 chr2:127783166-127783185
2	CTCF	chr2:127782074-127783952	SK-N-SH	brain:	n/a	chr2:127783230-127783246 chr2:127783266-127783279 chr2:127783537-127783550 chr2:127782458-127782471
3	CTCF	chr2:127782309-127782539	MCF-7	breast:	n/a	chr2:127782458-127782471
4	ZNF143	chr2:127782312-127783501	H1-hESC	embryonic stem cell:	n/a	chr2:127782434-127782453
5	MAX	chr2:127782186-127783539	H1-hESC	embryonic stem cell:	n/a	chr2:127782933-127782942 chr2:127782811-127782821 chr2:127783013-127783023
6	MXI1	chr2:127781934-127783919	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr2:127782110-127783740	IMR90	lung:	n/a	n/a
8	BACH1	chr2:127782317-127782632	H1-hESC	embryonic stem cell:	n/a	n/a
9	RAD21	chr2:127782215-127782715	H1-hESC	embryonic stem cell:	n/a	chr2:127782248-127782262
10	CTCF	chr2:127782314-127782593	H1-hESC	embryonic stem cell:	n/a	chr2:127782458-127782471
11	CTCF	chr2:127782198-127782630	IMR90	lung:	n/a	chr2:127782458-127782471
12	CTCF	chr2:127782320-127782470	HEK293	kidney:	n/a	n/a
13	USF2	chr2:127782305-127783084	H1-hESC	embryonic stem cell:	n/a	chr2:127782677-127782693
14	REST	chr2:127782142-127783796	H1-neurons	neurons:	n/a	chr2:127783111-127783124 chr2:127782677-127782687 chr2:127783528-127783541
15	CTCF	chr2:127782320-127782470	HMF	breast:	n/a	n/a
16	KAP1	chr2:127782247-127783728	U2OS	brain:	n/a	n/a
17	CTCF	chr2:127781993-127783826	A549	lung:	n/a	chr2:127783230-127783246 chr2:127783266-127783279 chr2:127783537-127783550 chr2:127782458-127782471
18	SIN3A	chr2:127782220-127783620	H1-hESC	embryonic stem cell:	n/a	chr2:127782367-127782377
19	MXI1	chr2:127782181-127782904	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr2:127782308-127783659	H1-neurons	neurons:	n/a	n/a
21	E2F6	chr2:127782202-127783617	H1-hESC	embryonic stem cell:	n/a	chr2:127782465-127782475 chr2:127783562-127783569 chr2:127783562-127783569 chr2:127783562-127783569
22	RAD21	chr2:127782285-127783388	H1-hESC	embryonic stem cell:	n/a	chr2:127782999-127783011 chr2:127782817-127782826 chr2:127783266-127783280
23	TAF1	chr2:127782306-127783461	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr2:127782225-127783593	H1-hESC	embryonic stem cell:	n/a	n/a
25	RFX5	chr2:127782039-127784240	SK-N-SH	brain:	n/a	n/a
26	CTCF	chr2:127782276-127782620	H1-hESC	embryonic stem cell:	n/a	chr2:127782458-127782471
27	JUN	chr2:127782134-127782533	H1-hESC	embryonic stem cell:	n/a	n/a
28	MAX	chr2:127782200-127783012	H1-hESC	embryonic stem cell:	n/a	chr2:127782933-127782942 chr2:127782811-127782821
29	CTCF	chr2:127782251-127782768	H1-hESC	embryonic stem cell:	n/a	chr2:127782458-127782471
30	KAP1	chr2:127782230-127783820	HEK293	kidney:	n/a	n/a
31	E2F6	chr2:127782308-127783474	H1-hESC	embryonic stem cell:	n/a	chr2:127782465-127782475
32	MAX	chr2:127782205-127783786	A549	lung:	n/a	chr2:127782933-127782942 chr2:127782811-127782821 chr2:127783013-127783023
33	CTBP2	chr2:127782265-127783356	H1-hESC	embryonic stem cell:	n/a	n/a
34	MAX	chr2:127782170-127783668	H1-hESC	embryonic stem cell:	n/a	chr2:127782933-127782942 chr2:127782811-127782821 chr2:127783013-127783023
35	CTCF	chr2:127782320-127782470	NHEK	skin:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-BIN1-1	chr2:127781828-127783299	ENSG00000260634.1

Variant related genes	Relation type
ENSG00000260163	TF binding region

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12476995	0.82[EUR][1000 genomes]
rs12611852	0.81[EUR][1000 genomes]
rs1438150	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1438151	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2404176	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3768863	0.86[EUR][1000 genomes]
rs3768865	0.81[EUR][1000 genomes]
rs56971880	0.83[EUR][1000 genomes]
rs59338031	0.84[EUR][1000 genomes]
rs6713701	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6724137	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6728529	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6736518	0.82[EUR][1000 genomes]
rs7571480	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7572041	0.81[EUR][1000 genomes]
rs893435	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9636241	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv834365	chr2:127616996-127793863	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv834366	chr2:127633714-127784692	Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	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
6	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4663088	BIN1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:127780400-127782800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr2:127781000-127782600	Weak transcription	Right Atrium	heart
3	chr2:127782000-127783600	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr2:127782200-127782400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr2:127782200-127782400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr2:127782200-127782400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr2:127782200-127782400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr2:127782200-127782400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr2:127782200-127782400	Enhancers	Muscle Satellite Cultured Cells	--
10	chr2:127782200-127782400	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr2:127782200-127782400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr2:127782200-127782400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr2:127782200-127782400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr2:127782200-127782400	Enhancers	Brain Hippocampus Middle	brain
15	chr2:127782200-127782400	Enhancers	Fetal Brain Male	brain
16	chr2:127782200-127782400	Enhancers	Fetal Intestine Large	intestine
17	chr2:127782200-127782400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
18	chr2:127782200-127782400	Enhancers	Ovary	ovary
19	chr2:127782200-127782400	Bivalent Enhancer	Rectal Smooth Muscle	rectum
20	chr2:127782200-127782400	Enhancers	Stomach Smooth Muscle	stomach
21	chr2:127782200-127782400	Enhancers	Spleen	Spleen
22	chr2:127782200-127782400	Enhancers	NH-A	brain
23	chr2:127782200-127782400	Flanking Active TSS	Osteobl	bone
24	chr2:127782200-127782600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr2:127782200-127782600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr2:127782200-127782600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr2:127782200-127782600	Active TSS	Breast Myoepithelial Primary Cells	Breast
28	chr2:127782200-127782600	Active TSS	Brain Angular Gyrus	brain
29	chr2:127782200-127782600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
30	chr2:127782200-127782600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
31	chr2:127782200-127782600	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
32	chr2:127782200-127782600	Bivalent Enhancer	Fetal Heart	heart
33	chr2:127782200-127782600	Active TSS	Fetal Lung	lung
34	chr2:127782200-127782600	Bivalent Enhancer	Fetal Muscle Leg	muscle
35	chr2:127782200-127782600	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
36	chr2:127782200-127782600	Active TSS	HMEC	breast
37	chr2:127782200-127782800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr2:127782200-127782800	Flanking Active TSS	Brain Cingulate Gyrus	brain
39	chr2:127782200-127782800	Active TSS	Colon Smooth Muscle	Colon
40	chr2:127782200-127783000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr2:127782200-127783000	Enhancers	Gastric	stomach
42	chr2:127782200-127783200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr2:127782200-127783200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr2:127782200-127783400	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr2:127782200-127783400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr2:127782200-127783400	Active TSS	Fetal Kidney	kidney
47	chr2:127782200-127783600	Active TSS	H9 Cell Line	embryonic stem cell
48	chr2:127782200-127783600	Active TSS	HUES6 Cell Line	embryonic stem cell
49	chr2:127782200-127783600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr2:127782200-127783600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin

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