Variant report

Variant	rs12280028
Chromosome Location	chr11:46576160-46576161
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:46574681..46577552-chr11:46580209..46581969,4	K562	blood:
2	chr11:46570718..46573249-chr11:46575495..46578902,3	MCF-7	breast:
3	chr11:46571213..46573722-chr11:46574368..46578173,3	K562	blood:
4	chr11:46571794..46573722-chr11:46574368..46577233,2	K562	blood:
5	chr11:46574208..46579341-chr11:46636969..46640425,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000180423	Chromatin interaction
ENSG00000175224	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11038894	0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs12280656	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs12295608	1.00[ASW][hapmap];1.00[LWK][hapmap];0.92[MKK][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1873130	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs56977210	0.81[AFR][1000 genomes]
rs6485680	0.91[ASW][hapmap];0.85[LWK][hapmap];0.81[MKK][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs73466034	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs73466036	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs73467915	0.90[AFR][1000 genomes]
rs7946094	0.81[AFR][1000 genomes];0.87[AMR][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	nsv1044225	chr11:46472580-46771102	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv541030	chr11:46472580-46771102	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats 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 miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1046990	chr11:46501436-46669636	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv541031	chr11:46501436-46669636	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv897321	chr11:46515902-46673344	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:46565000-46579200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr11:46566000-46579200	Weak transcription	Fetal Heart	heart
3	chr11:46567400-46576200	Weak transcription	Aorta	Aorta
4	chr11:46567400-46579000	Weak transcription	Pancreas	Pancrea
5	chr11:46567400-46579200	Weak transcription	Gastric	stomach
6	chr11:46567800-46576200	Weak transcription	Colonic Mucosa	Colon
7	chr11:46568000-46576400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr11:46568800-46576400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr11:46568800-46579000	Weak transcription	Lung	lung
10	chr11:46568800-46582200	Weak transcription	Fetal Stomach	stomach
11	chr11:46568800-46611000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr11:46568800-46612600	Weak transcription	Brain Germinal Matrix	brain
13	chr11:46569000-46576400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr11:46569000-46579000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr11:46569000-46579200	Weak transcription	Esophagus	oesophagus
16	chr11:46569000-46579200	Weak transcription	Spleen	Spleen
17	chr11:46569200-46576200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr11:46569200-46576400	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr11:46569400-46576200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr11:46569400-46576800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr11:46569600-46581400	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr11:46569800-46581400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr11:46570000-46576800	Weak transcription	Primary B cells from peripheral blood	blood
24	chr11:46570000-46581800	Weak transcription	Thymus	Thymus
25	chr11:46570000-46582000	Weak transcription	Fetal Muscle Leg	muscle
26	chr11:46570000-46582600	Weak transcription	Fetal Muscle Trunk	muscle
27	chr11:46574400-46577000	Enhancers	Monocytes-CD14+_RO01746	blood
28	chr11:46574600-46577400	Enhancers	Placenta	Placenta
29	chr11:46574600-46578000	Enhancers	Fetal Intestine Large	intestine
30	chr11:46574600-46578200	Enhancers	Fetal Intestine Small	intestine
31	chr11:46574800-46576800	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr11:46574800-46576800	Enhancers	NHLF	lung
33	chr11:46574800-46577000	Enhancers	Primary neutrophils fromperipheralblood	blood
34	chr11:46574800-46577000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr11:46574800-46577000	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr11:46574800-46577000	Flanking Active TSS	A549	lung
37	chr11:46574800-46577000	Enhancers	NH-A	brain
38	chr11:46574800-46577400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr11:46574800-46578000	Enhancers	Primary hematopoietic stem cells short term culture	blood
40	chr11:46574800-46578000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr11:46574800-46578000	Enhancers	Stomach Mucosa	stomach
42	chr11:46574800-46578400	Enhancers	Primary T helper cells fromperipheralblood	blood
43	chr11:46574800-46579600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
44	chr11:46574800-46580000	Enhancers	K562	blood
45	chr11:46574800-46581800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr11:46575000-46576400	Enhancers	Adipose Nuclei	Adipose
47	chr11:46575000-46576400	Enhancers	Duodenum Mucosa	Duodenum
48	chr11:46575000-46576600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr11:46575000-46576800	Enhancers	Primary hematopoietic stem cells	blood
50	chr11:46575000-46577000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links