Variant report

Variant	rs9653202
Chromosome Location	chr2:127867107-127867108
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	MAX	chr2:127866748-127867262	NB4	blood:	n/a	n/a
2	POLR2A	chr2:127866830-127867343	U87	brain:	n/a	n/a
3	EP300	chr2:127866892-127867325	SK-N-SH_RA	brain:	n/a	chr2:127867044-127867058
4	REST	chr2:127866888-127867380	PFSK-1	brain:	n/a	n/a
5	POLR2A	chr2:127866944-127867313	IMR90	lung:	n/a	n/a
6	MYC	chr2:127866791-127867275	NB4	blood:	n/a	n/a
7	FAM48A	chr2:127867016-127867141	GM12878	blood:	n/a	n/a
8	EBF1	chr2:127866888-127867239	GM12878	blood:	n/a	chr2:127867083-127867092 chr2:127867081-127867094
9	EP300	chr2:127866470-127867571	SK-N-SH	brain:	n/a	chr2:127867044-127867058
10	POLR2A	chr2:127866874-127867320	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr2:127866745-127867417	U87	brain:	n/a	n/a
12	POLR2A	chr2:127866983-127867342	SK-N-MC	brain:	n/a	n/a
13	EP300	chr2:127866687-127867269	SK-N-SH_RA	brain:	n/a	chr2:127867044-127867058
14	REST	chr2:127866865-127867262	PFSK-1	brain:	n/a	n/a
15	POLR2A	chr2:127866847-127867287	PFSK-1	brain:	n/a	n/a
16	POLR2A	chr2:127866745-127867423	U87	brain:	n/a	n/a
17	SIN3AK20	chr2:127866962-127867247	PFSK-1	brain:	n/a	n/a
18	POLR2A	chr2:127867013-127867310	SK-N-SH	brain:	n/a	n/a
19	POLR2A	chr2:127866908-127867434	PFSK-1	brain:	n/a	n/a
20	TCF12	chr2:127866617-127867422	SK-N-SH	brain:	n/a	n/a
21	MXI1	chr2:127866521-127867503	SK-N-SH	brain:	n/a	n/a
22	POLR2A	chr2:127866855-127867343	U87	brain:	n/a	n/a
23	POLR2A	chr2:127866911-127867269	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:127865657..127869658-chr2:127871080..127873352,3	K562	blood:

Variant related genes	Relation type
BIN1	TF binding region

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10198772	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10204965	0.96[ASN][1000 genomes]
rs11674215	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11674273	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11683933	0.94[EUR][1000 genomes]
rs11688714	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11688763	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11692858	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11695202	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13416395	0.96[ASN][1000 genomes]
rs13417002	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13417187	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13419729	0.96[ASN][1000 genomes]
rs13427080	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3845673	0.96[ASN][1000 genomes]
rs56772251	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56827597	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56853185	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6751498	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72959054	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72959055	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72959057	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72959066	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72959067	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs749009	0.97[EUR][1000 genomes]
rs7575579	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7583814	0.84[ASN][1000 genomes]
rs7584040	0.84[ASN][1000 genomes]
rs7600660	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7604081	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9653201	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9653203	1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9653206	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
rs9653202	BIN1	cis	multi-tissue	Pritchard

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:127865600-127867400	Enhancers	Primary B cells from peripheral blood	blood
2	chr2:127865600-127867400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr2:127865600-127867400	Enhancers	Placenta	Placenta
4	chr2:127865600-127867600	Enhancers	Adipose Nuclei	Adipose
5	chr2:127865600-127867600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr2:127865600-127868400	Weak transcription	Hela-S3	cervix
7	chr2:127865800-127867200	Enhancers	Fetal Intestine Small	intestine
8	chr2:127865800-127867200	Enhancers	Fetal Muscle Leg	muscle
9	chr2:127865800-127873000	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr2:127866000-127867200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr2:127866000-127867400	Enhancers	Brain Anterior Caudate	brain
12	chr2:127866000-127867600	Enhancers	Brain Substantia Nigra	brain
13	chr2:127866000-127868600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr2:127866000-127868600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr2:127866200-127868600	Weak transcription	Liver	Liver
16	chr2:127866200-127872400	Weak transcription	Fetal Intestine Large	intestine
17	chr2:127866200-127873200	Weak transcription	Gastric	stomach
18	chr2:127866400-127867200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr2:127866400-127867400	Enhancers	Muscle Satellite Cultured Cells	--
20	chr2:127866400-127867600	Enhancers	Primary B cells from cord blood	blood
21	chr2:127866600-127867200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr2:127866600-127867200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr2:127866600-127867200	Enhancers	HSMM	muscle
24	chr2:127866600-127867400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr2:127866800-127867200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr2:127866800-127867200	Flanking Active TSS	Brain Angular Gyrus	brain
27	chr2:127866800-127867200	Flanking Active TSS	Brain Cingulate Gyrus	brain
28	chr2:127866800-127867200	Flanking Active TSS	NH-A	brain
29	chr2:127866800-127867200	Flanking Active TSS	NHDF-Ad	bronchial
30	chr2:127866800-127867200	Flanking Active TSS	Osteobl	bone
31	chr2:127866800-127867400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
32	chr2:127866800-127867400	Enhancers	Fetal Lung	lung
33	chr2:127866800-127872600	Weak transcription	Fetal Muscle Trunk	muscle
34	chr2:127867000-127867200	Enhancers	Primary hematopoietic stem cells	blood
35	chr2:127867000-127867200	Flanking Active TSS	Brain Hippocampus Middle	brain
36	chr2:127867000-127867200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr2:127867000-127867200	Enhancers	Colon Smooth Muscle	Colon
38	chr2:127867000-127867200	Enhancers	A549	lung
39	chr2:127867000-127867200	Enhancers	HUVEC	blood vessel
40	chr2:127867000-127867200	Flanking Active TSS	NHLF	lung
41	chr2:127867000-127867400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr2:127867000-127867600	Enhancers	Brain Inferior Temporal Lobe	brain

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