Variant report

Variant	rs6672284
Chromosome Location	chr1:155277963-155277964
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:29)
CpG islands
(count:0)
Chromatin interactive
region (count:23)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:29 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:155277233-155280150	GM12891	blood:	n/a	n/a
2	POLR2A	chr1:155277191-155280041	GM12878	blood:	n/a	n/a
3	RUNX3	chr1:155277790-155279141	GM12878	blood:	n/a	n/a
4	POLR2A	chr1:155277427-155280155	K562	blood:	n/a	n/a
5	RPC155	chr1:155277476-155278358	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr1:155277342-155279740	Raji	blood:	n/a	n/a
7	NR2F2	chr1:155277236-155279209	K562	blood:	n/a	n/a
8	RPC155	chr1:155277313-155278369	K562	blood:	n/a	n/a
9	CTCF	chr1:155276834-155279064	SK-N-SH	brain:	n/a	n/a
10	TCF12	chr1:155277934-155279581	A549	lung:	n/a	n/a
11	POLR2A	chr1:155277861-155280126	HUVEC	blood vessel:	n/a	n/a
12	POLR2A	chr1:155277865-155280052	PFSK-1	brain:	n/a	n/a
13	MXI1	chr1:155277919-155279750	IMR90	lung:	n/a	n/a
14	PML	chr1:155277963-155279594	GM12878	blood:	n/a	n/a
15	POLR2A	chr1:155277255-155280173	K562	blood:	n/a	n/a
16	HCFC1	chr1:155277918-155280047	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr1:155277797-155278952	GM12878	blood:	n/a	n/a
18	FOXM1	chr1:155277623-155278845	GM12878	blood:	n/a	n/a
19	POLR2A	chr1:155277867-155280115	GM12878	blood:	n/a	n/a
20	KAP1	chr1:155277943-155278957	HEK293	kidney:	n/a	n/a
21	ZNF384	chr1:155277822-155278453	GM12878	blood:	n/a	n/a
22	E2F6	chr1:155277866-155278013	K562	blood:	n/a	n/a
23	POLR2A	chr1:155277059-155280809	SK-N-MC	brain:	n/a	n/a
24	ZNF384	chr1:155277299-155278604	K562	blood:	n/a	n/a
25	SREBP2	chr1:155277759-155279477	GM12878	blood:	n/a	n/a
26	POLR2A	chr1:155276996-155283922	HepG2	liver:	n/a	n/a
27	NFIC	chr1:155277961-155278776	GM12878	blood:	n/a	n/a
28	HEY1	chr1:155277958-155279768	HepG2	liver:	n/a	n/a
29	SP1	chr1:155277927-155279110	HCT-116	colon:	n/a	chr1:155278468-155278489

No data

(count:23 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:155245586..155250751-chr1:155275814..155280484,11	K562	blood:
2	chr1:155241469..155243385-chr1:155277012..155279531,3	MCF-7	breast:
3	chr1:155240186..155244594-chr1:155276068..155280700,10	MCF-7	breast:
4	chr1:154945299..154947459-chr1:155277553..155279453,2	K562	blood:
5	chr1:155179163..155181119-chr1:155277191..155279761,2	K562	blood:
6	chr1:155270303..155273300-chr1:155273424..155278245,4	MCF-7	breast:
7	chr1:155241171..155245021-chr1:155277000..155280071,7	K562	blood:
8	chr1:155195759..155198427-chr1:155276824..155279493,2	K562	blood:
9	chr1:155228693..155233633-chr1:155276892..155283389,6	K562	blood:
10	chr1:155245052..155250020-chr1:155276306..155280611,10	MCF-7	breast:
11	chr1:155270092..155273127-chr1:155275751..155279798,4	K562	blood:
12	chr1:155220296..155222214-chr1:155276999..155278896,2	K562	blood:
13	chr1:155277883..155278734-chr10:27442544..27443384,2	Hela-S3	cervix:
14	chr1:155246042..155249168-chr1:155274467..155279979,9	MCF-7	breast:
15	chr1:155162165..155164633-chr1:155276991..155278874,2	K562	blood:
16	chr1:155195750..155198407-chr1:155276763..155279696,2	K562	blood:
17	chr1:155223569..155227620-chr1:155275954..155279861,5	K562	blood:
18	chr1:155245770..155249042-chr1:155274997..155278484,6	K562	blood:
19	chr1:155221948..155224777-chr1:155277014..155278574,2	MCF-7	breast:
20	chr1:155220090..155222745-chr1:155275911..155279698,3	K562	blood:
21	chr1:155223569..155226696-chr1:155275954..155279861,6	K562	blood:
22	chr1:155238212..155240823-chr1:155276858..155278738,2	K562	blood:
23	chr1:155241810..155244486-chr1:155276710..155279928,5	K562	blood:

No data

Variant related genes	Relation type
FDPS	TF binding region
ENSG00000185499	Chromatin interaction
ENSG00000116521	Chromatin interaction
ENSG00000160691	Chromatin interaction
ENSG00000160767	Chromatin interaction
ENSG00000173171	Chromatin interaction
ENSG00000160766	Chromatin interaction
ENSG00000176444	Chromatin interaction
ENSG00000143627	Chromatin interaction
ENSG00000173207	Chromatin interaction
ENSG00000143630	Chromatin interaction
ENSG00000136758	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1046188	0.83[AMR][1000 genomes]
rs1052176	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1052177	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1076556	0.83[AMR][1000 genomes]
rs1078699	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs10796941	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10908461	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10908462	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10908463	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11264348	0.84[AMR][1000 genomes]
rs11264349	0.87[EUR][1000 genomes]
rs11264352	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11264353	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11264354	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11264355	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11264357	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11264358	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11264359	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11264361	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1142287	0.83[AMR][1000 genomes]
rs12032720	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12042020	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12044063	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12049375	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12067675	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12563994	0.83[AMR][1000 genomes]
rs12724449	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12749306	0.88[EUR][1000 genomes]
rs2071053	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2236863	0.85[AMR][1000 genomes]
rs2236864	0.86[AMR][1000 genomes]
rs2242576	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2297480	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2361543	0.85[AMR][1000 genomes]
rs3020781	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3814318	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3814319	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4620533	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4971072	0.98[ASN][1000 genomes]
rs7520184	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7524950	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7534795	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7543234	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7549276	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7554780	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8177968	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8847	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs932972	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9729564	0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757756	chr1:155094978-155314807	Bivalent Enhancer Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	452 gene(s)	inside rSNPs	diseases
2	esv2758971	chr1:155094978-155314807	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	452 gene(s)	inside rSNPs	diseases
3	nsv872457	chr1:155135335-155310443	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	407 gene(s)	inside rSNPs	diseases
4	nsv831625	chr1:155145634-155313409	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	407 gene(s)	inside rSNPs	diseases
5	nsv529709	chr1:155154933-155757219	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	450 gene(s)	inside rSNPs	diseases
6	nsv831636	chr1:155219223-155444864	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
7	esv33869	chr1:155223283-155917961	Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6672284	PKLR	cis	Nerve Tibial	GTEx
rs6672284	FDPS	Cis_1M	lymphoblastoid	RTeQTL
rs6672284	GBAP1	cis	Artery Tibial	GTEx
rs6672284	THBS3	cis	Whole Blood	GTEx
rs6672284	GBA	cis	Esophagus Mucosa	GTEx
rs6672284	RIT1	Cis_1M	lymphoblastoid	RTeQTL
rs6672284	GBAP1	cis	Thyroid	GTEx

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155270800-155278600	Weak transcription	Small Intestine	intestine
2	chr1:155275000-155278000	Weak transcription	Fetal Intestine Large	intestine
3	chr1:155275800-155278000	Weak transcription	A549	lung
4	chr1:155276000-155278000	Weak transcription	Duodenum Mucosa	Duodenum
5	chr1:155276000-155278600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr1:155276200-155278000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr1:155276200-155278000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr1:155276200-155278600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:155276200-155278600	Weak transcription	Esophagus	oesophagus
10	chr1:155276400-155278000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr1:155276400-155278400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr1:155276400-155278600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:155276600-155278000	Weak transcription	HSMM	muscle
14	chr1:155277000-155278000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr1:155277200-155278000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr1:155277200-155278000	Enhancers	Primary B cells from peripheral blood	blood
17	chr1:155277200-155278000	Enhancers	Fetal Muscle Leg	muscle
18	chr1:155277400-155278000	Enhancers	iPS-20b Cell Line	embryonic stem cell
19	chr1:155277400-155278000	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr1:155277400-155278000	Enhancers	Primary T cells fromperipheralblood	blood
21	chr1:155277400-155278000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr1:155277400-155278000	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr1:155277400-155278000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr1:155277400-155278000	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr1:155277400-155278000	Enhancers	Fetal Stomach	stomach
26	chr1:155277400-155278000	Enhancers	Fetal Thymus	thymus
27	chr1:155277400-155278000	Enhancers	Stomach Mucosa	stomach
28	chr1:155277400-155278000	Enhancers	Thymus	Thymus
29	chr1:155277400-155278000	Flanking Active TSS	GM12878-XiMat	blood
30	chr1:155277400-155278000	Enhancers	HMEC	breast
31	chr1:155277400-155278000	Weak transcription	NHDF-Ad	bronchial
32	chr1:155277400-155278200	Enhancers	HUVEC	blood vessel
33	chr1:155277400-155281000	Active TSS	HSMMtube	muscle
34	chr1:155277600-155278000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr1:155277600-155278000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr1:155277600-155278000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr1:155277600-155278000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
38	chr1:155277600-155278000	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr1:155277600-155278000	Enhancers	Brain Anterior Caudate	brain
40	chr1:155277600-155278000	Enhancers	Left Ventricle	heart
41	chr1:155277600-155278000	Enhancers	Lung	lung
42	chr1:155277600-155278000	Enhancers	Pancreas	Pancrea
43	chr1:155277600-155278000	Enhancers	NHLF	lung
44	chr1:155277600-155278000	Enhancers	Osteobl	bone
45	chr1:155277600-155278200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr1:155277600-155278200	Enhancers	Fetal Brain Male	brain
47	chr1:155277600-155278200	Flanking Active TSS	Placenta	Placenta
48	chr1:155277600-155278400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
49	chr1:155277600-155278400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr1:155277600-155278400	Flanking Active TSS	Dnd41	blood

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