Variant report

Variant	rs932054
Chromosome Location	chr1:150539867-150539868
allele	C/G
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	CHD1	chr1:150539859-150541588	H1-hESC	embryonic stem cell:	n/a	chr1:150540331-150540341
2	EBF1	chr1:150539670-150541315	GM12878	blood:	n/a	n/a
3	RCOR1	chr1:150539742-150540826	GM12878	blood:	n/a	n/a
4	EP300	chr1:150539775-150540531	GM12878	blood:	n/a	chr1:150540237-150540246
5	NFATC1	chr1:150539680-150541136	GM12878	blood:	n/a	n/a
6	RUNX3	chr1:150539585-150540995	GM12878	blood:	n/a	n/a
7	MEF2A	chr1:150539650-150540454	GM12878	blood:	n/a	chr1:150540240-150540248
8	MAX	chr1:150539694-150540934	GM12878	blood:	n/a	n/a
9	RELA	chr1:150539687-150540531	GM15510	blood:	n/a	n/a
10	RELA	chr1:150539728-150541172	GM10847	blood:	n/a	n/a
11	STAT2	chr1:150539798-150540360	K562	blood:	n/a	chr1:150540015-150540029 chr1:150539981-150539996
12	POLR2A	chr1:150538973-150541826	GM12891	blood:	n/a	n/a
13	POLR2A	chr1:150538992-150539987	Hela-S3	cervix:	n/a	n/a
14	TCF12	chr1:150539732-150540563	GM12878	blood:	n/a	chr1:150540320-150540327
15	POU2F2	chr1:150539596-150540871	GM12891	blood:	n/a	chr1:150540604-150540615
16	POLR2A	chr1:150538698-150546656	H1-hESC	embryonic stem cell:	n/a	n/a
17	ZNF263	chr1:150539711-150540328	HEK293-T-REx	kidney:	n/a	chr1:150539977-150539998 chr1:150539866-150539875
18	TBP	chr1:150539793-150540753	GM12878	blood:	n/a	n/a
19	POLR2A	chr1:150538889-150552727	K562	blood:	n/a	n/a
20	POLR2A	chr1:150538866-150546573	U87	brain:	n/a	n/a
21	STAT3	chr1:150539730-150540757	GM12878	blood:	n/a	chr1:150540015-150540029 chr1:150540016-150540027 chr1:150540011-150540032 chr1:150540625-150540636
22	POLR2A	chr1:150539774-150546448	HUVEC	blood vessel:	n/a	n/a
23	NFIC	chr1:150539585-150541059	GM12878	blood:	n/a	n/a
24	EP300	chr1:150539774-150540467	GM12878	blood:	n/a	chr1:150540237-150540246
25	POU2F2	chr1:150539690-150540595	GM12878	blood:	n/a	n/a
26	CHD2	chr1:150539706-150540975	GM12878	blood:	n/a	chr1:150540331-150540341
27	POLR2A	chr1:150527732-150552686	MCF10A-Er-Src	breast:	n/a	n/a
28	PAX5	chr1:150539668-150540509	GM12878	blood:	n/a	n/a
29	MEF2C	chr1:150539624-150540430	GM12878	blood:	n/a	chr1:150540240-150540248
30	ZNF384	chr1:150539680-150540431	GM12878	blood:	n/a	n/a
31	POLR2A	chr1:150530622-150553130	IMR90	lung:	n/a	n/a
32	SP1	chr1:150539703-150540765	GM12878	blood:	n/a	chr1:150540582-150540593 chr1:150540329-150540341 chr1:150540331-150540340
33	NFIC	chr1:150539583-150540902	GM12878	blood:	n/a	n/a
34	POLR2A	chr1:150539675-150540003	GM12878	blood:	n/a	n/a
35	POLR2A	chr1:150538654-150552953	Hela-S3	cervix:	n/a	n/a
36	EBF1	chr1:150539664-150540109	GM12878	blood:	n/a	n/a
37	BCL11A	chr1:150539763-150540118	GM12878	blood:	n/a	n/a
38	ETS1	chr1:150539715-150540547	GM12878	blood:	n/a	n/a
39	POLR2A	chr1:150539740-150539895	H1-hESC	embryonic stem cell:	n/a	n/a
40	BCLAF1	chr1:150539702-150540934	GM12878	blood:	n/a	chr1:150540625-150540634
41	POLR2A	chr1:150539749-150541722	K562	blood:	n/a	n/a
42	POLR2A	chr1:150539052-150541758	K562	blood:	n/a	n/a
43	POLR2A	chr1:150539727-150546572	HepG2	liver:	n/a	n/a
44	POLR2A	chr1:150539702-150540985	Raji	blood:	n/a	n/a
45	EP300	chr1:150539760-150540784	GM12878	blood:	n/a	chr1:150540237-150540246
46	POLR2A	chr1:150530539-150552850	MCF10A-Er-Src	breast:	n/a	n/a
47	POLR2A	chr1:150539558-150541740	GM19193	blood:	n/a	n/a
48	POLR2A	chr1:150538736-150552926	GM12878	blood:	n/a	n/a
49	CEBPB	chr1:150539311-150540800	GM12878	blood:	n/a	n/a
50	MTA3	chr1:150539566-150541051	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:150538740..150540797-chr1:150784272..150785983,2	MCF-7	breast:
2	chr1:150538995..150557554-chr1:150581886..150604495,126	K562	blood:
3	chr1:150531290..150540028-chr1:150591374..150603951,29	MCF-7	breast:
4	chr1:150539815..150542556-chr1:150853753..150855583,2	K562	blood:
5	chr1:150539334..150542207-chr1:150782861..150785483,3	K562	blood:
6	chr1:150539071..150540911-chr1:150952638..150955044,2	MCF-7	breast:
7	chr1:150520253..150522845-chr1:150539005..150541527,2	MCF-7	breast:
8	chr1:150459936..150462426-chr1:150537781..150540425,2	K562	blood:
9	chr1:150539334..150542207-chr1:150782861..150785483,4	K562	blood:
10	chr1:150458168..150459777-chr1:150539728..150541445,2	MCF-7	breast:

Variant related genes	Relation type
RN7SL473P	TF binding region
ENSG00000200175	Chromatin interaction
ENSG00000225996	Chromatin interaction
ENSG00000143382	Chromatin interaction
ENSG00000143412	Chromatin interaction
ENSG00000143420	Chromatin interaction
ENSG00000143374	Chromatin interaction
ENSG00000212512	Chromatin interaction
ENSG00000224800	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10888384	0.85[ASN][1000 genomes]
rs10888385	0.85[ASN][1000 genomes]
rs11204668	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11204669	0.89[ASN][1000 genomes]
rs11204675	0.85[ASN][1000 genomes]
rs11204677	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11204678	0.83[ASN][1000 genomes]
rs11204679	0.85[ASN][1000 genomes]
rs11204680	0.85[ASN][1000 genomes]
rs11585169	0.85[ASN][1000 genomes]
rs12116492	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12125672	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12126271	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12139563	0.83[ASN][1000 genomes]
rs12406712	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12746899	0.85[ASN][1000 genomes]
rs2048558	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3738484	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3738485	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4970918	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4971041	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55862611	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61820165	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6697620	0.85[ASN][1000 genomes]
rs6698495	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs878471	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9803935	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006838	chr1:150440214-150722783	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
2	esv1814231	chr1:150479528-150540117	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	71 gene(s)	inside rSNPs	diseases
3	nsv527379	chr1:150527354-150542128	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
4	nsv535155	chr1:150535349-150582395	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs932054	RP11-316M1.12	cis	Adipose Subcutaneous	GTEx
rs932054	HORMAD1	cis	Nerve Tibial	GTEx
rs932054	HORMAD1	cis	Adipose Subcutaneous	GTEx
rs932054	ARNT	Cis_1M	lymphoblastoid	RTeQTL
rs932054	HORMAD1	cis	Esophagus Mucosa	GTEx
rs932054	ARNT	cis	Thyroid	GTEx
rs932054	GOLPH3L	cis	Nerve Tibial	GTEx
rs932054	HORMAD1	cis	Skin Sun Exposed Lower leg	GTEx
rs932054	GOLPH3L	cis	Skin Sun Exposed Lower leg	GTEx
rs932054	RNU6-1042P	cis	Esophagus Mucosa	GTEx
rs932054	CTSS	Cis_1M	lymphoblastoid	RTeQTL
rs932054	CTSK	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150534400-150547200	Weak transcription	Ovary	ovary
2	chr1:150534600-150540200	Enhancers	Pancreas	Pancrea
3	chr1:150534600-150542600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:150534600-150542600	Enhancers	Lung	lung
5	chr1:150534800-150540400	Enhancers	Sigmoid Colon	Sigmoid Colon
6	chr1:150535000-150540000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr1:150535000-150540200	Enhancers	Left Ventricle	heart
8	chr1:150535000-150542200	Enhancers	Placenta	Placenta
9	chr1:150535200-150540000	Enhancers	Fetal Intestine Large	intestine
10	chr1:150535200-150540000	Enhancers	Psoas Muscle	Psoas
11	chr1:150535200-150540000	Enhancers	Right Atrium	heart
12	chr1:150535200-150541000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
13	chr1:150535200-150541800	Enhancers	Small Intestine	intestine
14	chr1:150535400-150540200	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr1:150535400-150540400	Enhancers	Fetal Heart	heart
16	chr1:150535600-150540200	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr1:150536000-150540800	Enhancers	Stomach Mucosa	stomach
18	chr1:150536600-150540600	Weak transcription	Fetal Brain Female	brain
19	chr1:150536800-150540400	Weak transcription	Fetal Brain Male	brain
20	chr1:150537200-150540000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr1:150537600-150540000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr1:150538200-150540200	Enhancers	Spleen	Spleen
23	chr1:150538200-150540400	Enhancers	Right Ventricle	heart
24	chr1:150538400-150540200	Enhancers	Brain Anterior Caudate	brain
25	chr1:150538600-150540000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr1:150538800-150540000	Enhancers	Aorta	Aorta
27	chr1:150538800-150540000	Enhancers	Fetal Stomach	stomach
28	chr1:150538800-150541800	Flanking Active TSS	GM12878-XiMat	blood
29	chr1:150538800-150541800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
30	chr1:150538800-150543800	Enhancers	Placenta Amnion	Placenta Amnion
31	chr1:150538800-150543800	Enhancers	HMEC	breast
32	chr1:150539000-150540000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr1:150539000-150540000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:150539000-150540000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr1:150539000-150540000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr1:150539000-150540000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr1:150539000-150540000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
38	chr1:150539000-150540000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
39	chr1:150539000-150540000	Enhancers	Brain Cingulate Gyrus	brain
40	chr1:150539000-150540000	Enhancers	HepG2	liver
41	chr1:150539000-150540200	Enhancers	H1 Cell Line	embryonic stem cell
42	chr1:150539000-150541200	Enhancers	Brain Substantia Nigra	brain
43	chr1:150539000-150541600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
44	chr1:150539000-150541600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
45	chr1:150539000-150541600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr1:150539000-150541800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
47	chr1:150539000-150542000	Flanking Active TSS	Primary T cells from cord blood	blood
48	chr1:150539000-150542400	Flanking Active TSS	Primary B cells from cord blood	blood
49	chr1:150539000-150543000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
50	chr1:150539200-150540000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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