Variant report

Variant	rs411828
Chromosome Location	chr12:118741714-118741715
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:118740466..118742711-chr12:118813102..118814672,2	MCF-7	breast:
2	chr12:118728193..118730845-chr12:118739160..118741836,2	K562	blood:

Variant related genes	Relation type
ENSG00000270482	Chromatin interaction
ENSG00000111707	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1151900	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs168497	0.84[ASN][1000 genomes]
rs1699160	0.94[EUR][1000 genomes]
rs1726390	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs191626	0.88[EUR][1000 genomes]
rs2650175	0.86[EUR][1000 genomes]
rs353884	0.86[EUR][1000 genomes]
rs353888	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs353891	0.81[EUR][1000 genomes]
rs353893	0.88[EUR][1000 genomes]
rs353894	0.87[EUR][1000 genomes]
rs353895	0.83[EUR][1000 genomes]
rs353897	0.88[EUR][1000 genomes]
rs383371	0.88[EUR][1000 genomes]
rs424034	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs428073	0.81[EUR][1000 genomes]
rs431038	0.86[EUR][1000 genomes]
rs459547	0.85[EUR][1000 genomes]
rs461801	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs464227	0.90[EUR][1000 genomes]
rs556081	0.91[EUR][1000 genomes]
rs61945179	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs708865	0.87[EUR][1000 genomes]
rs708867	0.87[EUR][1000 genomes]
rs708868	0.87[EUR][1000 genomes]
rs795476	0.84[EUR][1000 genomes]
rs811247	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053785	chr12:118490955-118874194	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv1038224	chr12:118648415-118791388	Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1040061	chr12:118648415-118800437	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1053417	chr12:118688969-118808530	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:118676000-118745200	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr12:118693400-118745000	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr12:118702600-118744600	Weak transcription	Duodenum Mucosa	Duodenum
4	chr12:118712400-118745000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr12:118719200-118744400	Weak transcription	HSMM	muscle
6	chr12:118720800-118793600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr12:118722600-118745000	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr12:118726600-118746800	Weak transcription	Lung	lung
9	chr12:118728400-118744400	Weak transcription	NHLF	lung
10	chr12:118731200-118744400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr12:118732600-118744800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr12:118732800-118767600	Weak transcription	Primary T cells from cord blood	blood
13	chr12:118733400-118745000	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr12:118735000-118744600	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr12:118735400-118744400	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr12:118735600-118745000	Weak transcription	Primary B cells from cord blood	blood
17	chr12:118736200-118746000	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr12:118736600-118742600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr12:118738000-118742000	Enhancers	NHEK	skin
20	chr12:118738000-118744600	Weak transcription	Fetal Intestine Small	intestine
21	chr12:118738000-118745000	Weak transcription	Small Intestine	intestine
22	chr12:118738200-118744400	Weak transcription	NH-A	brain
23	chr12:118738200-118745200	Weak transcription	Brain Hippocampus Middle	brain
24	chr12:118738200-118761800	Weak transcription	Fetal Lung	lung
25	chr12:118738400-118744800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr12:118738400-118745000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr12:118738600-118745200	Weak transcription	Brain Anterior Caudate	brain
28	chr12:118738600-118745600	Weak transcription	Brain Cingulate Gyrus	brain
29	chr12:118739000-118741800	Enhancers	NHDF-Ad	bronchial
30	chr12:118739000-118744800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr12:118739200-118749400	Weak transcription	Brain Angular Gyrus	brain
32	chr12:118739400-118743000	Enhancers	GM12878-XiMat	blood
33	chr12:118740000-118745000	Weak transcription	K562	blood
34	chr12:118740200-118742400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr12:118740200-118744600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr12:118740200-118744800	Weak transcription	Primary B cells from peripheral blood	blood
37	chr12:118740200-118745000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr12:118740200-118745000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr12:118740200-118745000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr12:118740200-118745000	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr12:118740400-118743800	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr12:118740400-118744200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr12:118740400-118744400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr12:118740400-118744400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr12:118740400-118744400	Weak transcription	Osteobl	bone
46	chr12:118740400-118744600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr12:118740400-118748800	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr12:118740600-118744200	Weak transcription	HUVEC	blood vessel
49	chr12:118740600-118745000	Weak transcription	Liver	Liver
50	chr12:118740800-118744800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links