Variant report

Variant	rs12117078
Chromosome Location	chr1:153929365-153929366
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	RCOR1	chr1:153929291-153929607	K562	blood:	n/a	n/a
2	NFYB	chr1:153929132-153929483	K562	blood:	n/a	chr1:153929281-153929295 chr1:153929281-153929296 chr1:153929281-153929296
3	WRNIP1	chr1:153928422-153930598	GM12878	blood:	n/a	n/a
4	POLR2A	chr1:153929336-153932363	GM12891	blood:	n/a	n/a
5	NFYB	chr1:153929136-153929493	GM12878	blood:	n/a	chr1:153929281-153929295 chr1:153929281-153929296 chr1:153929281-153929296
6	POLR2A	chr1:153929267-153931574	GM12878	blood:	n/a	n/a
7	MTA3	chr1:153929272-153931566	GM12878	blood:	n/a	n/a
8	BCLAF1	chr1:153929356-153929858	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:153767106..153771449-chr1:153928785..153931237,4	MCF-7	breast:
2	chr1:153635410..153637927-chr1:153928123..153932423,3	K562	blood:
3	chr1:153747107..153752136-chr1:153929206..153936862,9	MCF-7	breast:

Variant related genes	Relation type
CRTC2	TF binding region
ENSG00000143554	Chromatin interaction
ENSG00000231827	Chromatin interaction
ENSG00000143621	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10127484	1.00[JPT][hapmap]
rs10908578	1.00[JPT][hapmap]
rs11264573	1.00[JPT][hapmap]
rs11264736	1.00[JPT][hapmap]
rs11264972	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[LWK][hapmap]
rs12142733	1.00[JPT][hapmap]
rs17364880	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2230324	1.00[AFR][1000 genomes]
rs2252508	1.00[JPT][hapmap]
rs55874907	1.00[AFR][1000 genomes]
rs61804835	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6661009	1.00[JPT][hapmap]
rs7414227	1.00[JPT][hapmap]
rs7522030	1.00[JPT][hapmap]

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	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	nsv531892	chr1:153671910-153954090	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
4	nsv532551	chr1:153732039-154192279	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
5	esv1830240	chr1:153885261-154370938	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	239 gene(s)	inside rSNPs	diseases
6	nsv872450	chr1:153889042-153937513	Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS Weak 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	61 gene(s)	inside rSNPs	diseases
7	nsv532552	chr1:153912047-153950752	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12117078	PSMD4	cis	parietal	SCAN
rs12117078	INTS3	cis	lymphoblastoid	seeQTL
rs12117078	PI4KB	cis	cerebellum	SCAN
rs12117078	PGLYRP4	cis	cerebellum	SCAN
rs12117078	TMOD4	cis	parietal	SCAN
rs12117078	KCTD14	trans	lymphoblastoid	seeQTL
rs12117078	SLC27A3	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153919200-153929600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:153924600-153929800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:153925000-153929600	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr1:153925200-153929400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:153926000-153929400	Weak transcription	HSMM	muscle
6	chr1:153926200-153929400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr1:153927400-153929400	Enhancers	Skeletal Muscle Female	skeletal muscle
8	chr1:153927400-153929600	Weak transcription	HSMMtube	muscle
9	chr1:153927400-153929800	Enhancers	Right Ventricle	heart
10	chr1:153927600-153929400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr1:153927600-153929600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr1:153927600-153929800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr1:153928000-153929400	Enhancers	Primary B cells from peripheral blood	blood
14	chr1:153928000-153930000	Enhancers	Left Ventricle	heart
15	chr1:153928200-153929400	Enhancers	Primary neutrophils fromperipheralblood	blood
16	chr1:153928200-153929400	Enhancers	Brain Anterior Caudate	brain
17	chr1:153928200-153929400	Enhancers	Duodenum Smooth Muscle	Duodenum
18	chr1:153928200-153929400	Enhancers	Fetal Thymus	thymus
19	chr1:153928200-153929400	Enhancers	Sigmoid Colon	Sigmoid Colon
20	chr1:153928200-153929400	Enhancers	NHDF-Ad	bronchial
21	chr1:153928200-153929600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr1:153928200-153929600	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr1:153928200-153929600	Enhancers	Brain Substantia Nigra	brain
24	chr1:153928200-153929600	Enhancers	Rectal Mucosa Donor 31	rectum
25	chr1:153928200-153929800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr1:153928200-153929800	Enhancers	Fetal Muscle Leg	muscle
27	chr1:153928200-153930000	Enhancers	Small Intestine	intestine
28	chr1:153928200-153930200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
29	chr1:153928200-153930400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
30	chr1:153928400-153929400	Enhancers	Rectal Smooth Muscle	rectum
31	chr1:153928400-153929400	Flanking Active TSS	GM12878-XiMat	blood
32	chr1:153928400-153929400	Genic enhancers	NHEK	skin
33	chr1:153928400-153929600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr1:153928400-153929600	Enhancers	NH-A	brain
35	chr1:153928400-153929800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
36	chr1:153928400-153929800	Enhancers	Fetal Lung	lung
37	chr1:153928400-153929800	Enhancers	Fetal Muscle Trunk	muscle
38	chr1:153928400-153929800	Enhancers	Placenta	Placenta
39	chr1:153928400-153929800	Enhancers	Lung	lung
40	chr1:153928400-153929800	Enhancers	Psoas Muscle	Psoas
41	chr1:153928400-153929800	Enhancers	Right Atrium	heart
42	chr1:153928400-153930000	Enhancers	Aorta	Aorta
43	chr1:153928400-153930000	Enhancers	Pancreas	Pancrea
44	chr1:153928400-153930200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
45	chr1:153928400-153930200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
46	chr1:153928400-153930200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
47	chr1:153928400-153930200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
48	chr1:153928400-153930200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
49	chr1:153928400-153930400	Flanking Active TSS	Primary T cells from cord blood	blood
50	chr1:153928400-153930400	Flanking Active TSS	Primary hematopoietic stem cells	blood

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