Variant report

Variant	rs960117
Chromosome Location	chr12:46613819-46613820
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:46611489..46616057-chr12:46626284..46631509,6	MCF-7	breast:
2	chr12:46611672..46615140-chr12:46658386..46664443,5	K562	blood:
3	chr12:46608964..46611081-chr12:46612036..46613850,2	K562	blood:
4	chr12:46611743..46615456-chr12:46661323..46664567,5	MCF-7	breast:
5	chr12:46593049..46595554-chr12:46612027..46614436,2	MCF-7	breast:
6	chr12:46611766..46613913-chr12:46659130..46661605,2	MCF-7	breast:
7	chr12:46611447..46614258-chr12:46760762..46763199,2	K562	blood:

Variant related genes	Relation type
ENSG00000111371	Chromatin interaction
ENSG00000134294	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs4768106	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4768107	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6582622	1.00[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.89[MEX][hapmap];0.83[TSI][hapmap];0.97[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7971399	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs962683	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs963326	1.00[CHB][hapmap];0.84[GIH][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832398	chr12:46611692-46825530	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	181 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs960117	IRAK4	cis	cerebellum	SCAN
rs960117	SLC48A1	cis	cerebellum	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46592800-46654200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:46596000-46618200	Weak transcription	Aorta	Aorta
3	chr12:46597400-46614200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr12:46597600-46659600	Weak transcription	Colonic Mucosa	Colon
5	chr12:46604000-46623400	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr12:46604000-46633800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr12:46604000-46637400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:46604400-46618600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr12:46605000-46615000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr12:46605000-46615200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr12:46607000-46615000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr12:46608400-46615000	Enhancers	Primary hematopoietic stem cells	blood
13	chr12:46608400-46618200	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr12:46609000-46614400	Weak transcription	Fetal Stomach	stomach
15	chr12:46609200-46618600	Enhancers	Primary neutrophils fromperipheralblood	blood
16	chr12:46610200-46619000	Weak transcription	Psoas Muscle	Psoas
17	chr12:46610400-46624000	Weak transcription	Pancreas	Pancrea
18	chr12:46610600-46640000	Weak transcription	Esophagus	oesophagus
19	chr12:46610800-46614400	Weak transcription	Brain Germinal Matrix	brain
20	chr12:46611400-46615800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
21	chr12:46611600-46616800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr12:46612000-46615400	Strong transcription	Fetal Muscle Leg	muscle
23	chr12:46612000-46617200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr12:46612200-46615200	Enhancers	Fetal Intestine Small	intestine
25	chr12:46612200-46615200	Enhancers	Small Intestine	intestine
26	chr12:46612200-46616000	Enhancers	Placenta	Placenta
27	chr12:46612200-46618200	Genic enhancers	NHEK	skin
28	chr12:46612400-46614200	Enhancers	Dnd41	blood
29	chr12:46612400-46614400	Enhancers	Thymus	Thymus
30	chr12:46612400-46614600	Genic enhancers	H1 Cell Line	embryonic stem cell
31	chr12:46612400-46615400	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr12:46612400-46618400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr12:46612600-46618400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr12:46612800-46614400	Genic enhancers	Fetal Thymus	thymus
35	chr12:46613000-46616800	Genic enhancers	HUES64 Cell Line	embryonic stem cell
36	chr12:46613200-46614000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
37	chr12:46613200-46614000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
38	chr12:46613200-46614000	Enhancers	NHDF-Ad	bronchial
39	chr12:46613200-46614200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
40	chr12:46613200-46614200	Enhancers	Fetal Intestine Large	intestine
41	chr12:46613200-46614400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
42	chr12:46613200-46614400	Strong transcription	Fetal Brain Female	brain
43	chr12:46613200-46615400	Enhancers	HSMM	muscle
44	chr12:46613200-46615800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr12:46613200-46616000	Enhancers	Sigmoid Colon	Sigmoid Colon
46	chr12:46613200-46616200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr12:46613200-46616400	Genic enhancers	HUES48 Cell Line	embryonic stem cell
48	chr12:46613200-46616400	Genic enhancers	HUES6 Cell Line	embryonic stem cell
49	chr12:46613200-46617200	Genic enhancers	Hela-S3	cervix
50	chr12:46613200-46617400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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