Variant report

Variant	rs7139055
Chromosome Location	chr12:123364198-123364199
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:123363372..123365357-chr12:123379648..123382097,2	MCF-7	breast:
2	chr12:123356727..123361663-chr12:123362714..123365634,4	K562	blood:
3	chr12:123364125..123366940-chr12:123368799..123371711,4	K562	blood:
4	chr12:123362099..123364653-chr12:123375458..123377701,2	K562	blood:
5	chr12:123359999..123363082-chr12:123363364..123366412,4	MCF-7	breast:
6	chr12:123364142..123368499-chr12:123374436..123379970,6	K562	blood:

Variant related genes	Relation type
ENSG00000139722	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10744422	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10744434	1.00[EUR][1000 genomes]
rs10773627	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs10773657	0.91[EUR][1000 genomes]
rs10847826	0.85[EUR][1000 genomes]
rs10847869	0.91[EUR][1000 genomes]
rs12255	1.00[CEU][hapmap];0.97[GIH][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes]
rs12303328	0.85[CHB][hapmap];0.92[JPT][hapmap];0.93[ASN][1000 genomes]
rs12426809	0.91[EUR][1000 genomes]
rs1532835	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1587856	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2061098	0.95[CHB][hapmap];0.86[JPT][hapmap];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2061101	0.94[CHB][hapmap];0.86[JPT][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2135014	0.83[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2271050	1.00[CEU][hapmap];0.94[GIH][hapmap];0.82[TSI][hapmap]
rs2271051	0.82[MEX][hapmap]
rs2292132	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2292134	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2292135	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2292136	0.83[CEU][hapmap];0.82[AMR][1000 genomes]
rs2292138	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2343108	0.90[EUR][1000 genomes]
rs2343109	0.96[EUR][1000 genomes]
rs2343685	0.85[EUR][1000 genomes]
rs2880678	0.85[EUR][1000 genomes]
rs3817094	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3825143	0.92[CEU][hapmap];0.97[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs3852536	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3852537	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs4759355	1.00[CEU][hapmap];0.97[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs4759381	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4759382	1.00[CEU][hapmap];0.97[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs4759386	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4759387	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4759389	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs4759393	0.83[CEU][hapmap]
rs6489245	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs6489247	0.83[CEU][hapmap];0.90[CHB][hapmap]
rs7138398	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7294991	1.00[CEU][hapmap];0.85[TSI][hapmap]
rs7309225	1.00[CEU][hapmap];0.85[TSI][hapmap]
rs7957643	0.81[CEU][hapmap]
rs7959441	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7972447	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7980541	1.00[EUR][1000 genomes]
rs897385	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs897386	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs897391	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs897393	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs921808	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs936083	0.83[CEU][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs937766	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3388790	chr12:123275902-123655103	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv899572	chr12:123292503-123477311	Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv899573	chr12:123312051-123528405	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv517200	chr12:123312051-123654498	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
5	nsv899576	chr12:123335527-123528405	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' 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	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7139055	HIP1R	cis	parietal	SCAN
rs7139055	CCDC62	cis	cerebellum	SCAN
rs7139055	CCDC62	cis	Thyroid	GTEx
rs7139055	ACADS	cis	parietal	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123356200-123368600	Weak transcription	Hela-S3	cervix
2	chr12:123356600-123364200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr12:123356800-123369200	Enhancers	Primary T killer memory cells from peripheral blood	blood
4	chr12:123356800-123370000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr12:123357000-123365600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr12:123357000-123369800	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr12:123357000-123373000	Weak transcription	Aorta	Aorta
8	chr12:123357200-123365200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr12:123358200-123367200	Weak transcription	HUVEC	blood vessel
10	chr12:123358800-123371400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr12:123359000-123365000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr12:123359000-123365200	Weak transcription	Stomach Smooth Muscle	stomach
13	chr12:123359000-123368400	Weak transcription	Fetal Intestine Large	intestine
14	chr12:123359000-123369600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr12:123359400-123366000	Enhancers	Skeletal Muscle Female	skeletal muscle
16	chr12:123359600-123365000	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr12:123359600-123366200	Enhancers	Right Atrium	heart
18	chr12:123360400-123365400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr12:123360800-123364200	Weak transcription	Brain Anterior Caudate	brain
20	chr12:123360800-123364600	Enhancers	Spleen	Spleen
21	chr12:123360800-123364800	Weak transcription	Brain Angular Gyrus	brain
22	chr12:123360800-123364800	Weak transcription	Brain Cingulate Gyrus	brain
23	chr12:123360800-123368800	Weak transcription	Colon Smooth Muscle	Colon
24	chr12:123361200-123365400	Genic enhancers	Lung	lung
25	chr12:123361200-123365600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr12:123361400-123365400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr12:123361600-123364800	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr12:123361600-123365000	Weak transcription	NHDF-Ad	bronchial
29	chr12:123361600-123365200	Genic enhancers	Primary T helper cells PMA-I stimulated	--
30	chr12:123361600-123365200	Weak transcription	Fetal Brain Male	brain
31	chr12:123361600-123365600	Genic enhancers	Primary B cells from peripheral blood	blood
32	chr12:123361800-123364200	Weak transcription	Osteobl	bone
33	chr12:123361800-123364400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
34	chr12:123361800-123364800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr12:123361800-123365000	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr12:123361800-123365400	Genic enhancers	Fetal Thymus	thymus
37	chr12:123362000-123364200	Weak transcription	Fetal Lung	lung
38	chr12:123362000-123364200	Weak transcription	NHLF	lung
39	chr12:123362000-123364800	Enhancers	Primary T helper naive cells from peripheral blood	blood
40	chr12:123362000-123364800	Strong transcription	Fetal Stomach	stomach
41	chr12:123362000-123364800	Weak transcription	NH-A	brain
42	chr12:123362200-123364800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr12:123362200-123365800	Genic enhancers	Fetal Muscle Leg	muscle
44	chr12:123362200-123367600	Enhancers	Primary T cells from cord blood	blood
45	chr12:123362400-123364400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
46	chr12:123362400-123364600	Weak transcription	Brain Germinal Matrix	brain
47	chr12:123362400-123365000	Strong transcription	NHEK	skin
48	chr12:123362400-123365200	Weak transcription	Small Intestine	intestine
49	chr12:123362400-123365600	Strong transcription	HMEC	breast
50	chr12:123362400-123368400	Weak transcription	Liver	Liver

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