Variant report

Variant	rs1218584
Chromosome Location	chr1:154833067-154833068
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	RELA	chr1:154832089-154833412	GM18951	blood:	n/a	n/a
2	POLR2A	chr1:154831732-154833515	GM12892	blood:	n/a	n/a
3	NRF1	chr1:154832732-154833212	GM12878	blood:	n/a	n/a
4	POLR2A	chr1:154832100-154833297	GM10847	blood:	n/a	n/a
5	MEF2A	chr1:154832006-154833221	GM12878	blood:	n/a	chr1:154832377-154832388
6	RELA	chr1:154832127-154833346	GM12891	blood:	n/a	n/a
7	SIN3A	chr1:154832696-154833175	GM12878	blood:	n/a	n/a
8	POU2F2	chr1:154832052-154833358	GM12891	blood:	n/a	chr1:154832906-154832915 chr1:154832419-154832426 chr1:154832391-154832409 chr1:154832417-154832427 chr1:154832396-154832404 chr1:154832418-154832427 chr1:154832416-154832428 chr1:154832415-154832430 chr1:154832904-154832918 chr1:154832395-154832409 chr1:154832396-154832403 chr1:154832417-154832427 chr1:154832395-154832406 chr1:154832390-154832411 chr1:154832395-154832406 chr1:154832416-154832430 chr1:154832395-154832405 chr1:154832394-154832404 chr1:154832907-154832914 chr1:154832395-154832404 chr1:154832416-154832429 chr1:154832392-154832407
9	MYC	chr1:154832751-154833220	K562	blood:	n/a	n/a
10	STAT5A	chr1:154831325-154833441	GM12878	blood:	n/a	chr1:154832652-154832666 chr1:154832538-154832550
11	POLR2A	chr1:154831263-154833473	GM19099	blood:	n/a	n/a
12	BCL11A	chr1:154832720-154833151	GM12878	blood:	n/a	n/a
13	MAZ	chr1:154832264-154833322	GM12878	blood:	n/a	n/a
14	SPI1	chr1:154832879-154833147	K562	blood:	n/a	chr1:154833047-154833060
15	POLR2A	chr1:154831038-154833419	GM12878	blood:	n/a	n/a
16	EBF1	chr1:154832055-154833404	GM12878	blood:	n/a	chr1:154832974-154832985
17	CUX1	chr1:154832763-154833162	GM12878	blood:	n/a	n/a
18	EP300	chr1:154832247-154833444	GM12878	blood:	n/a	chr1:154833049-154833058
19	FOXM1	chr1:154832138-154833382	GM12878	blood:	n/a	n/a
20	RUNX3	chr1:154832042-154833500	GM12878	blood:	n/a	chr1:154832939-154832948
21	NFIC	chr1:154831990-154833411	GM12878	blood:	n/a	n/a
22	MTA3	chr1:154831744-154833490	GM12878	blood:	n/a	n/a
23	EBF1	chr1:154831785-154833414	GM12878	blood:	n/a	chr1:154832974-154832985
24	BHLHE40	chr1:154832873-154833237	K562	blood:	n/a	chr1:154833174-154833190
25	POLR2A	chr1:154831318-154833415	GM18505	blood:	n/a	n/a
26	POLR2A	chr1:154831351-154833435	GM15510	blood:	n/a	n/a
27	RELA	chr1:154832119-154833414	GM19099	blood:	n/a	n/a
28	SP1	chr1:154832642-154833347	GM12878	blood:	n/a	chr1:154833145-154833152
29	SPI1	chr1:154832802-154833249	GM12891	blood:	n/a	chr1:154833047-154833060
30	YY1	chr1:154832801-154833303	GM12878	blood:	n/a	n/a
31	BHLHE40	chr1:154832212-154833393	GM12878	blood:	n/a	chr1:154833174-154833190
32	RELA	chr1:154832127-154833379	GM19193	blood:	n/a	n/a
33	IKZF1	chr1:154832204-154833319	GM12878	blood:	n/a	n/a
34	ZNF384	chr1:154832860-154833457	GM12878	blood:	n/a	n/a
35	POLR2A	chr1:154832017-154833391	GM12878	blood:	n/a	n/a
36	TCF12	chr1:154832266-154833404	GM12878	blood:	n/a	chr1:154832549-154832559 chr1:154833283-154833290
37	POLR2A	chr1:154832082-154833371	GM12891	blood:	n/a	n/a
38	RUNX3	chr1:154831953-154833436	GM12878	blood:	n/a	chr1:154832939-154832948
39	STAT3	chr1:154832148-154833336	GM12878	blood:	n/a	chr1:154832652-154832666 chr1:154832538-154832550
40	ZEB1	chr1:154832698-154833331	GM12878	blood:	n/a	n/a
41	PAX5	chr1:154832795-154833252	GM12878	blood:	n/a	chr1:154833048-154833057
42	POU2F2	chr1:154832110-154833331	GM12878	blood:	n/a	chr1:154832906-154832915 chr1:154832419-154832426 chr1:154832391-154832409 chr1:154832417-154832427 chr1:154832396-154832404 chr1:154832418-154832427 chr1:154832416-154832428 chr1:154832415-154832430 chr1:154832904-154832918 chr1:154832395-154832409 chr1:154832396-154832403 chr1:154832417-154832427 chr1:154832395-154832406 chr1:154832390-154832411 chr1:154832395-154832406 chr1:154832416-154832430 chr1:154832395-154832405 chr1:154832394-154832404 chr1:154832907-154832914 chr1:154832395-154832404 chr1:154832416-154832429 chr1:154832392-154832407
43	USF2	chr1:154832713-154833329	GM12878	blood:	n/a	chr1:154833174-154833190
44	STAT5A	chr1:154832073-154833340	GM12878	blood:	n/a	chr1:154832652-154832666 chr1:154832538-154832550
45	SPI1	chr1:154832583-154833399	GM12878	blood:	n/a	chr1:154833047-154833060
46	RELA	chr1:154832133-154833400	GM15510	blood:	n/a	n/a
47	ELF1	chr1:154832329-154833349	GM12878	blood:	n/a	n/a
48	BATF	chr1:154832179-154833312	GM12878	blood:	n/a	chr1:154832343-154832352
49	POLR2A	chr1:154831409-154833465	GM18951	blood:	n/a	n/a
50	FOXM1	chr1:154832243-154833421	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:154771337..154773585-chr1:154832415..154834960,2	MCF-7	breast:
2	chr1:154832792..154836317-chr1:154841340..154844437,3	K562	blood:

Variant related genes	Relation type
KCNN3	TF binding region
ENSG00000143603	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1061122	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10908443	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11264302	1.00[JPT][hapmap]
rs11264303	1.00[JPT][hapmap]
rs11582128	1.00[JPT][hapmap]
rs1218554	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1218585	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1218587	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1218588	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1218589	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1218592	1.00[ASN][1000 genomes]
rs12760148	1.00[CHB][hapmap]
rs16836525	1.00[CHB][hapmap]
rs2878412	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4845396	1.00[CHB][hapmap]
rs4845397	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4845402	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4845675	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6660884	1.00[JPT][hapmap]
rs6682335	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs906596	1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs906597	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.88[AMR][1000 genomes];0.86[EUR][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	nsv532579	chr1:154548165-155262692	Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	575 gene(s)	inside rSNPs	diseases
2	nsv427797	chr1:154559115-154933717	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv432931	chr1:154794318-154855055	Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
4	esv29982	chr1:154818353-154882544	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv432942	chr1:154818353-154903047	Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv432964	chr1:154820067-154849590	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
7	nsv432953	chr1:154820067-154855055	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1218584	LENEP	cis	cerebellum	SCAN
rs1218584	C1orf85	cis	parietal	SCAN
rs1218584	INTS3	cis	parietal	SCAN
rs1218584	BCAN	cis	parietal	SCAN
rs1218584	S100A7L2	cis	parietal	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154821000-154837200	Weak transcription	Colon Smooth Muscle	Colon
2	chr1:154822600-154838000	Weak transcription	Brain Angular Gyrus	brain
3	chr1:154824400-154834200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:154827600-154839400	Enhancers	Fetal Brain Male	brain
5	chr1:154827800-154833600	Enhancers	Fetal Muscle Leg	muscle
6	chr1:154828000-154833400	Enhancers	Brain Anterior Caudate	brain
7	chr1:154828400-154833400	Flanking Active TSS	GM12878-XiMat	blood
8	chr1:154830600-154833400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
9	chr1:154830800-154834000	Strong transcription	Fetal Stomach	stomach
10	chr1:154831200-154839800	Enhancers	Psoas Muscle	Psoas
11	chr1:154831400-154839400	Enhancers	Primary B cells from peripheral blood	blood
12	chr1:154831600-154833400	Enhancers	Brain Germinal Matrix	brain
13	chr1:154831600-154835200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr1:154831800-154833400	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr1:154831800-154833400	Enhancers	Right Ventricle	heart
16	chr1:154831800-154835800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
17	chr1:154831800-154839400	Enhancers	Fetal Thymus	thymus
18	chr1:154832000-154833200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr1:154832000-154833200	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr1:154832000-154834400	Enhancers	Thymus	Thymus
21	chr1:154832000-154834800	Enhancers	Primary B cells from cord blood	blood
22	chr1:154832000-154837000	Enhancers	HSMM	muscle
23	chr1:154832200-154834200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr1:154832200-154836600	Enhancers	Muscle Satellite Cultured Cells	--
25	chr1:154832400-154833200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr1:154832400-154833200	Enhancers	Left Ventricle	heart
27	chr1:154832400-154834000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr1:154832400-154834600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr1:154832400-154840000	Enhancers	K562	blood
30	chr1:154832600-154833200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr1:154832600-154833200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr1:154832600-154833200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr1:154832600-154833200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
34	chr1:154832600-154833200	Enhancers	NH-A	brain
35	chr1:154832600-154833400	Enhancers	Primary hematopoietic stem cells short term culture	blood
36	chr1:154832600-154833400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
37	chr1:154832800-154833200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
38	chr1:154832800-154833400	Enhancers	Primary hematopoietic stem cells	blood
39	chr1:154832800-154834800	Weak transcription	Brain Cingulate Gyrus	brain
40	chr1:154832800-154835400	Enhancers	Fetal Brain Female	brain
41	chr1:154832800-154835800	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr1:154832800-154836600	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr1:154832800-154837800	Enhancers	HSMMtube	muscle
44	chr1:154833000-154833200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr1:154833000-154833200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr1:154833000-154833200	Enhancers	Osteobl	bone
47	chr1:154833000-154833400	Enhancers	Brain Substantia Nigra	brain
48	chr1:154833000-154833400	Enhancers	Lung	lung
49	chr1:154833000-154833400	Weak transcription	Spleen	Spleen
50	chr1:154833000-154833400	Enhancers	Monocytes-CD14+_RO01746	blood

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