Variant report

Variant	rs12418162
Chromosome Location	chr11:107885991-107885992
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:107883045..107885752-chr11:107885908..107888287,2	MCF-7	breast:
2	chr11:107879275..107881405-chr11:107882359..107886354,4	MCF-7	breast:
3	chr11:107878975..107881021-chr11:107884748..107886581,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166266	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11212483	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11604711	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11607588	0.82[CHB][hapmap];0.85[CHD][hapmap]
rs12416788	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12421527	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12793438	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12796482	0.93[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs15677	1.00[CHB][hapmap]
rs35185685	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35237843	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs60762047	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs71464788	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533794	chr11:107349817-108093259	Bivalent Enhancer Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv1039425	chr11:107468681-107895836	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv1049524	chr11:107540937-107954011	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv521771	chr11:107590335-107904646	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv1048938	chr11:107604473-107929950	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	18 gene(s)	inside rSNPs	diseases
6	esv2750980	chr11:107720941-107970986	Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
7	nsv1047984	chr11:107794729-107950746	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer 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 target site	13 gene(s)	inside rSNPs	diseases
8	nsv1040345	chr11:107824764-107924309	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	9 gene(s)	inside rSNPs	diseases
9	esv3372573	chr11:107880365-108022895	Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12418162	KDELC2	cis	cerebellum	SCAN
rs12418162	CUL5	cis	frontal cortex	BrainEAC

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:107880800-107888400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr11:107880800-107890600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr11:107881000-107886200	Weak transcription	Pancreas	Pancrea
4	chr11:107881000-107891000	Weak transcription	Lung	lung
5	chr11:107881000-107904000	Weak transcription	Fetal Muscle Trunk	muscle
6	chr11:107881000-107904800	Weak transcription	Placenta	Placenta
7	chr11:107881200-107886800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr11:107881200-107887200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr11:107881200-107890000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr11:107881200-107890600	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr11:107881600-107896200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr11:107881600-107904600	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr11:107881800-107890400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr11:107882000-107886800	Weak transcription	Stomach Smooth Muscle	stomach
15	chr11:107882200-107886400	Weak transcription	Fetal Brain Female	brain
16	chr11:107882200-107887000	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr11:107882200-107887000	Weak transcription	Fetal Stomach	stomach
18	chr11:107882200-107888200	Weak transcription	Primary B cells from peripheral blood	blood
19	chr11:107882200-107889600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr11:107882200-107890000	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr11:107882200-107890000	Weak transcription	Hela-S3	cervix
22	chr11:107882200-107890200	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr11:107882200-107890600	Weak transcription	HSMMtube	muscle
24	chr11:107882200-107890600	Weak transcription	NHLF	lung
25	chr11:107882200-107894800	Weak transcription	Rectal Smooth Muscle	rectum
26	chr11:107882200-107896200	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr11:107882200-107896600	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr11:107882200-107904800	Weak transcription	Duodenum Mucosa	Duodenum
29	chr11:107882200-107904800	Weak transcription	Fetal Intestine Large	intestine
30	chr11:107882200-107907800	Weak transcription	Fetal Kidney	kidney
31	chr11:107882200-107908000	Weak transcription	A549	lung
32	chr11:107882200-107917000	Weak transcription	NH-A	brain
33	chr11:107882600-107906200	Weak transcription	Fetal Intestine Small	intestine
34	chr11:107883000-107896000	Weak transcription	Brain Hippocampus Middle	brain
35	chr11:107883400-107896000	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr11:107883600-107893400	Weak transcription	Right Ventricle	heart
37	chr11:107883800-107887000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr11:107883800-107887000	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr11:107883800-107890400	Weak transcription	Left Ventricle	heart
40	chr11:107883800-107890600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr11:107883800-107890800	Weak transcription	Small Intestine	intestine
42	chr11:107884000-107886600	Weak transcription	Liver	Liver
43	chr11:107884000-107896200	Weak transcription	Primary hematopoietic stem cells	blood
44	chr11:107884200-107886000	Weak transcription	Colon Smooth Muscle	Colon
45	chr11:107884200-107896000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr11:107884200-107904800	Weak transcription	HUVEC	blood vessel
47	chr11:107884400-107886000	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr11:107884400-107886000	Weak transcription	Gastric	stomach
49	chr11:107884400-107886600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr11:107884400-107886800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links