Variant report

Variant	rs12278619
Chromosome Location	chr11:102182049-102182050
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	chr11:102178580..102181050-chr11:102181151..102183123,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000271600	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10082693	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs10466639	1.00[AMR][1000 genomes]
rs11225219	1.00[AMR][1000 genomes]
rs11225223	1.00[AMR][1000 genomes]
rs11225228	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs11225245	1.00[AMR][1000 genomes]
rs11225246	1.00[AMR][1000 genomes]
rs11604189	1.00[YRI][hapmap]
rs12270723	1.00[AMR][1000 genomes]
rs12270893	1.00[AMR][1000 genomes]
rs12271569	1.00[AMR][1000 genomes]
rs12273819	1.00[AMR][1000 genomes]
rs12275349	1.00[YRI][hapmap]
rs12279712	1.00[AMR][1000 genomes]
rs12279854	1.00[AMR][1000 genomes]
rs12281328	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs12282509	1.00[YRI][hapmap]
rs12283520	1.00[AMR][1000 genomes]
rs12283923	1.00[AMR][1000 genomes]
rs12288938	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs12290870	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs12291114	1.00[YRI][hapmap]
rs12291210	1.00[YRI][hapmap]
rs12291456	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs12293263	1.00[AMR][1000 genomes]
rs12294170	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs12295864	1.00[AMR][1000 genomes]
rs12296030	1.00[AMR][1000 genomes]
rs12792649	1.00[YRI][hapmap]
rs13377309	1.00[AMR][1000 genomes]
rs13377312	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs36039928	1.00[AMR][1000 genomes]
rs9971623	1.00[AMR][1000 genomes]

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	nsv1052348	chr11:101987090-102255753	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv556141	chr11:101988061-102207851	Weak transcription Genic enhancers Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv1050961	chr11:101993880-102253717	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv1051735	chr11:101993880-102255753	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv530646	chr11:102000840-102238992	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	esv3514195	chr11:102118479-102348362	Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	esv3514197	chr11:102118479-102348362	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:102173200-102182400	Weak transcription	Gastric	stomach
2	chr11:102173600-102183800	Weak transcription	Lung	lung
3	chr11:102176800-102187800	Weak transcription	Pancreas	Pancrea
4	chr11:102177000-102187800	Weak transcription	Spleen	Spleen
5	chr11:102177200-102187000	Weak transcription	Colonic Mucosa	Colon
6	chr11:102177600-102183400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr11:102177600-102183800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr11:102178000-102184000	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr11:102178200-102183000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr11:102178200-102183000	Weak transcription	HepG2	liver
11	chr11:102178200-102183200	Weak transcription	Duodenum Mucosa	Duodenum
12	chr11:102178200-102183400	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr11:102178200-102183400	Weak transcription	Fetal Lung	lung
14	chr11:102178200-102183600	Weak transcription	NH-A	brain
15	chr11:102178200-102183800	Weak transcription	Fetal Intestine Large	intestine
16	chr11:102178200-102183800	Weak transcription	Left Ventricle	heart
17	chr11:102178200-102183800	Weak transcription	Psoas Muscle	Psoas
18	chr11:102178200-102188000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr11:102178400-102182800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr11:102178400-102182800	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr11:102178400-102183000	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr11:102178400-102183200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr11:102178400-102183200	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr11:102178400-102183400	Weak transcription	Brain Cingulate Gyrus	brain
25	chr11:102178400-102183400	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr11:102178400-102183600	Weak transcription	Placenta	Placenta
27	chr11:102178400-102183800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr11:102178400-102183800	Weak transcription	Stomach Mucosa	stomach
29	chr11:102178400-102187200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr11:102178400-102187800	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr11:102178600-102183400	Weak transcription	Primary hematopoietic stem cells	blood
32	chr11:102178600-102183800	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr11:102178800-102183000	Weak transcription	HMEC	breast
34	chr11:102178800-102183200	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr11:102179400-102183000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr11:102179600-102182400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr11:102179600-102182600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr11:102179600-102182600	Weak transcription	Dnd41	blood
39	chr11:102179600-102183000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr11:102179600-102183400	Weak transcription	Primary T cells from cord blood	blood
41	chr11:102179600-102183400	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr11:102179600-102183400	Weak transcription	A549	lung
43	chr11:102180800-102183000	Weak transcription	Hela-S3	cervix
44	chr11:102180800-102183200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr11:102180800-102183200	Weak transcription	NHEK	skin
46	chr11:102181000-102183400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr11:102181200-102182200	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr11:102181400-102183400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
49	chr11:102181600-102183000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
50	chr11:102181600-102183400	Enhancers	Primary T regulatory cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links