Variant report

Variant	rs2356298
Chromosome Location	chr3:51534721-51534722
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	POLR2A	chr3:51532964-51534754	U87	brain:	n/a	n/a
2	POLR2A	chr3:51532934-51534761	SK-N-MC	brain:	n/a	n/a
3	PAX5	chr3:51534399-51534799	GM12878	blood:	n/a	n/a
4	POLR2A	chr3:51532986-51534727	PFSK-1	brain:	n/a	n/a
5	ELF1	chr3:51533008-51534898	HCT-116	colon:	n/a	chr3:51534330-51534339 chr3:51533143-51533154 chr3:51533722-51533734 chr3:51534329-51534340
6	POLR2A	chr3:51532915-51534761	HUVEC	blood vessel:	n/a	n/a
7	CBX3	chr3:51533847-51534861	K562	blood:	n/a	n/a
8	CREB1	chr3:51533085-51534830	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr3:51533020-51534760	GM12891	blood:	n/a	n/a
10	HCFC1	chr3:51532583-51534805	Hela-S3	cervix:	n/a	n/a
11	CTCF	chr3:51534640-51534790	HCPEpiC	choroid plexus:	n/a	n/a
12	POLR2A	chr3:51533164-51534723	HUVEC	blood vessel:	n/a	n/a
13	ELF1	chr3:51533025-51534769	HCT-116	colon:	n/a	chr3:51534330-51534339 chr3:51533143-51533154 chr3:51533722-51533734 chr3:51534329-51534340
14	POLR2A	chr3:51533115-51534834	HepG2	liver:	n/a	n/a
15	RCOR1	chr3:51533821-51534741	Hela-S3	cervix:	n/a	n/a
16	SP1	chr3:51532960-51534747	HCT-116	colon:	n/a	chr3:51533600-51533609 chr3:51533353-51533362 chr3:51533787-51533796 chr3:51533675-51533685 chr3:51533600-51533609 chr3:51533786-51533795 chr3:51533675-51533684 chr3:51533675-51533689 chr3:51533786-51533796 chr3:51533600-51533610 chr3:51533749-51533758 chr3:51533352-51533364 chr3:51534211-51534223 chr3:51533785-51533796 chr3:51533747-51533759 chr3:51534302-51534323 chr3:51533748-51533757 chr3:51533600-51533610 chr3:51533599-51533611 chr3:51533352-51533364 chr3:51533600-51533614 chr3:51533676-51533685 chr3:51534211-51534223 chr3:51533785-51533797 chr3:51533354-51533363 chr3:51533851-51533864 chr3:51533747-51533759 chr3:51533675-51533684 chr3:51533674-51533686 chr3:51534213-51534222 chr3:51533786-51533800 chr3:51533599-51533611 chr3:51533601-51533610 chr3:51533674-51533686 chr3:51533785-51533797 chr3:51533728-51533742 chr3:51533747-51533758 chr3:51533675-51533685
17	ELF1	chr3:51533187-51534751	MCF-7	breast:	n/a	chr3:51534330-51534339 chr3:51533722-51533734 chr3:51534329-51534340
18	POLR2A	chr3:51533183-51534727	Raji	blood:	n/a	n/a
19	ZNF263	chr3:51533926-51534827	HEK293-T-REx	kidney:	n/a	n/a
20	POLR2A	chr3:51533134-51534725	GM18951	blood:	n/a	n/a
21	ZNF384	chr3:51533197-51534769	K562	blood:	n/a	n/a
22	MXI1	chr3:51532856-51534785	SK-N-SH	brain:	n/a	n/a
23	POLR2A	chr3:51532990-51534737	Hela-S3	cervix:	n/a	n/a
24	SREBP1	chr3:51532518-51534791	GM12878	blood:	n/a	n/a
25	EP300	chr3:51533407-51534814	GM12878	blood:	n/a	chr3:51534329-51534343
26	POLR2A	chr3:51533783-51534748	U87	brain:	n/a	n/a
27	CREB1	chr3:51533197-51534867	GM12878	blood:	n/a	n/a
28	SP1	chr3:51533014-51534754	HCT-116	colon:	n/a	chr3:51533600-51533609 chr3:51533353-51533362 chr3:51533787-51533796 chr3:51533675-51533685 chr3:51533600-51533609 chr3:51533786-51533795 chr3:51533675-51533684 chr3:51533675-51533689 chr3:51533786-51533796 chr3:51533600-51533610 chr3:51533749-51533758 chr3:51533352-51533364 chr3:51534211-51534223 chr3:51533785-51533796 chr3:51533747-51533759 chr3:51534302-51534323 chr3:51533748-51533757 chr3:51533600-51533610 chr3:51533599-51533611 chr3:51533352-51533364 chr3:51533600-51533614 chr3:51533676-51533685 chr3:51534211-51534223 chr3:51533785-51533797 chr3:51533354-51533363 chr3:51533851-51533864 chr3:51533747-51533759 chr3:51533675-51533684 chr3:51533674-51533686 chr3:51534213-51534222 chr3:51533786-51533800 chr3:51533599-51533611 chr3:51533601-51533610 chr3:51533674-51533686 chr3:51533785-51533797 chr3:51533728-51533742 chr3:51533747-51533758 chr3:51533675-51533685
29	ELF1	chr3:51533041-51534766	SK-N-SH	brain:	n/a	chr3:51534330-51534339 chr3:51533143-51533154 chr3:51533722-51533734 chr3:51534329-51534340
30	NRF1	chr3:51532986-51534723	SK-N-SH	brain:	n/a	chr3:51533601-51533610 chr3:51534053-51534067 chr3:51534055-51534064 chr3:51533676-51533685
31	RCOR1	chr3:51533167-51534731	HepG2	liver:	n/a	n/a
32	POLR2A	chr3:51533136-51534759	GM19193	blood:	n/a	n/a
33	POLR2A	chr3:51533104-51534757	H1-hESC	embryonic stem cell:	n/a	n/a
34	SETDB1	chr3:51534324-51534829	U2OS	brain:	n/a	n/a
35	POLR2A	chr3:51533189-51534756	GM12878	blood:	n/a	n/a
36	ELF1	chr3:51533049-51534873	GM12878	blood:	n/a	chr3:51534330-51534339 chr3:51533143-51533154 chr3:51533722-51533734 chr3:51534329-51534340
37	POLR2A	chr3:51534224-51534750	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:51420258..51423192-chr3:51532829..51535179,2	K562	blood:
2	chr3:51534170..51537061-chr3:51667512..51669238,2	MCF-7	breast:
3	chr3:51532560..51534895-chr3:51704003..51706915,3	K562	blood:
4	chr3:51532457..51535099-chr3:51703667..51706623,4	MCF-7	breast:
5	chr3:51421541..51423885-chr3:51533443..51535010,2	K562	blood:
6	chr3:51533144..51535964-chr3:51704671..51707377,2	MCF-7	breast:
7	chr3:51533596..51535948-chr3:51713544..51717803,3	K562	blood:
8	chr3:51426988..51429067-chr3:51532869..51536301,5	K562	blood:
9	chr3:51532744..51536241-chr3:51571123..51575595,5	K562	blood:
10	chr3:51427878..51430154-chr3:51533292..51535600,2	MCF-7	breast:
11	chr3:51532096..51536424-chr3:51702408..51707498,7	K562	blood:
12	chr3:51428575..51432934-chr3:51531325..51537191,8	K562	blood:

Variant related genes	Relation type
VPRBP	TF binding region
ENSG00000164081	Chromatin interaction
ENSG00000179837	Chromatin interaction
ENSG00000145050	Chromatin interaction
ENSG00000164080	Chromatin interaction

Extended variants
information (count: 105 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs10510757	1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap];0.88[ASN][1000 genomes]
rs10510758	0.94[ASN][1000 genomes]
rs12485610	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12486568	0.83[ASN][1000 genomes]
rs12487426	1.00[ASN][1000 genomes]
rs12487468	0.94[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap];0.89[ASN][1000 genomes]
rs12489414	0.95[ASN][1000 genomes]
rs12490471	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12490889	0.89[ASN][1000 genomes]
rs12491048	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12492624	1.00[ASN][1000 genomes]
rs12493265	0.98[ASN][1000 genomes]
rs12493618	0.95[ASN][1000 genomes]
rs12493857	1.00[ASN][1000 genomes]
rs12493978	0.94[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap];0.89[ASN][1000 genomes]
rs12494462	1.00[ASN][1000 genomes]
rs12494979	0.94[ASN][1000 genomes]
rs13089799	0.86[ASN][1000 genomes]
rs13090348	0.95[ASN][1000 genomes]
rs1370124	0.92[ASN][1000 genomes]
rs17051783	0.94[ASN][1000 genomes]
rs17051811	0.95[ASN][1000 genomes]
rs17661242	0.94[ASN][1000 genomes]
rs17712228	0.95[ASN][1000 genomes]
rs1842394	0.94[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs2033703	0.95[ASN][1000 genomes]
rs2082992	0.99[ASN][1000 genomes]
rs2082993	0.98[ASN][1000 genomes]
rs2170177	0.83[CHB][hapmap];0.83[CHD][hapmap];0.89[MEX][hapmap]
rs2217938	0.94[ASN][1000 genomes]
rs2241785	0.92[ASN][1000 genomes]
rs2304512	0.94[ASN][1000 genomes]
rs2306430	0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2306431	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.89[ASN][1000 genomes]
rs2356261	0.94[ASN][1000 genomes]
rs35536327	0.95[ASN][1000 genomes]
rs3749317	0.94[ASN][1000 genomes]
rs3792408	0.94[ASN][1000 genomes]
rs3804766	0.94[ASN][1000 genomes]
rs3828395	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.91[ASN][1000 genomes]
rs4468966	0.94[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap];0.84[ASN][1000 genomes]
rs4687553	0.96[ASN][1000 genomes]
rs4687563	0.98[ASN][1000 genomes]
rs4687566	1.00[EUR][1000 genomes]
rs4687599	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs4687601	0.94[ASN][1000 genomes]
rs4687605	1.00[ASN][1000 genomes]
rs4687610	0.95[ASN][1000 genomes]
rs4687656	0.99[ASN][1000 genomes]
rs4687691	0.97[ASN][1000 genomes]
rs4687731	0.94[ASN][1000 genomes]
rs4687777	0.94[ASN][1000 genomes]
rs4687794	0.97[ASN][1000 genomes]
rs4687811	0.95[ASN][1000 genomes]
rs4687812	0.94[ASN][1000 genomes]
rs4687813	0.94[ASN][1000 genomes]
rs4974096	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.89[ASN][1000 genomes]
rs55667499	0.98[ASN][1000 genomes]
rs55671465	0.91[ASN][1000 genomes]
rs56239081	1.00[ASN][1000 genomes]
rs56729479	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57027950	0.95[ASN][1000 genomes]
rs57047724	0.88[ASN][1000 genomes]
rs57603251	0.85[ASN][1000 genomes]
rs57700326	0.81[ASN][1000 genomes]
rs57831708	0.92[ASN][1000 genomes]
rs58059174	1.00[ASN][1000 genomes]
rs58189274	0.88[ASN][1000 genomes]
rs58201844	0.84[ASN][1000 genomes]
rs58568178	0.94[ASN][1000 genomes]
rs58762652	0.81[ASN][1000 genomes]
rs58836277	0.94[ASN][1000 genomes]
rs59563413	0.88[ASN][1000 genomes]
rs59564034	0.83[ASN][1000 genomes]
rs59838596	0.98[ASN][1000 genomes]
rs59953568	0.89[ASN][1000 genomes]
rs60007226	0.83[ASN][1000 genomes]
rs60606339	1.00[ASN][1000 genomes]
rs61233013	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61419317	0.94[ASN][1000 genomes]
rs61689323	0.98[ASN][1000 genomes]
rs72945708	0.88[ASN][1000 genomes]
rs72945713	0.92[ASN][1000 genomes]
rs72951443	0.98[ASN][1000 genomes]
rs73834252	0.94[ASN][1000 genomes]
rs73834253	0.98[ASN][1000 genomes]
rs73834254	0.98[ASN][1000 genomes]
rs73834258	1.00[ASN][1000 genomes]
rs73837439	0.89[ASN][1000 genomes]
rs73837442	0.94[ASN][1000 genomes]
rs73837443	0.94[ASN][1000 genomes]
rs751076	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.84[ASN][1000 genomes]
rs7642698	0.95[ASN][1000 genomes]
rs880478	0.94[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs9817077	0.94[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap];0.83[ASN][1000 genomes]
rs9817872	0.94[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap];0.83[ASN][1000 genomes]
rs9819195	0.94[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs9820140	0.92[ASN][1000 genomes]
rs9827186	0.95[ASN][1000 genomes]
rs9829057	0.94[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap];0.84[ASN][1000 genomes]
rs9842600	0.97[ASN][1000 genomes]
rs9843583	0.96[ASN][1000 genomes]
rs9856134	0.94[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.89[MEX][hapmap];0.83[ASN][1000 genomes]
rs9861019	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014464	chr3:51220151-51909780	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51532400-51534800	Active TSS	Psoas Muscle	Psoas
2	chr3:51532600-51534800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr3:51532600-51534800	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr3:51532600-51534800	Active TSS	iPS-15b Cell Line	embryonic stem cell
5	chr3:51532600-51534800	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr3:51532600-51534800	Active TSS	A549	lung
7	chr3:51532800-51534800	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr3:51532800-51534800	Active TSS	iPS-18 Cell Line	embryonic stem cell
9	chr3:51532800-51534800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr3:51532800-51534800	Active TSS	Fetal Intestine Large	intestine
11	chr3:51532800-51534800	Active TSS	HSMMtube	muscle
12	chr3:51533000-51534800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:51533000-51534800	Active TSS	HUES64 Cell Line	embryonic stem cell
14	chr3:51533000-51534800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr3:51533000-51534800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr3:51533000-51534800	Active TSS	Brain Hippocampus Middle	brain
17	chr3:51533000-51534800	Active TSS	Colonic Mucosa	Colon
18	chr3:51533000-51534800	Active TSS	Right Ventricle	heart
19	chr3:51533000-51534800	Active TSS	NH-A	brain
20	chr3:51533200-51534800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr3:51533200-51534800	Active TSS	Brain Germinal Matrix	brain
22	chr3:51533200-51534800	Active TSS	Brain Inferior Temporal Lobe	brain
23	chr3:51533200-51534800	Active TSS	Duodenum Mucosa	Duodenum
24	chr3:51533200-51534800	Active TSS	Osteobl	bone
25	chr3:51533200-51535000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr3:51534200-51534800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr3:51534200-51534800	Flanking Active TSS	Primary B cells from cord blood	blood
28	chr3:51534200-51534800	Flanking Active TSS	Dnd41	blood
29	chr3:51534200-51535200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr3:51534400-51534800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr3:51534400-51534800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
32	chr3:51534400-51534800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
33	chr3:51534400-51534800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
34	chr3:51534400-51534800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
35	chr3:51534400-51534800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
36	chr3:51534400-51534800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
37	chr3:51534400-51534800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
38	chr3:51534400-51534800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
39	chr3:51534400-51534800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr3:51534400-51534800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr3:51534400-51534800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
42	chr3:51534400-51534800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
43	chr3:51534400-51534800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr3:51534400-51534800	Flanking Active TSS	Adipose Nuclei	Adipose
45	chr3:51534400-51534800	Flanking Active TSS	Brain Cingulate Gyrus	brain
46	chr3:51534400-51534800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
47	chr3:51534400-51534800	Flanking Active TSS	Fetal Lung	lung
48	chr3:51534400-51534800	Flanking Active TSS	Placenta	Placenta
49	chr3:51534400-51534800	Flanking Active TSS	Fetal Thymus	thymus
50	chr3:51534400-51534800	Enhancers	Placenta Amnion	Placenta Amnion

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