Variant report

Variant	rs1228031
Chromosome Location	chr11:48035474-48035475
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:47868355..47870814-chr11:48034909..48036899,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000030066	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1228026	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1228028	1.00[ASW][hapmap];0.88[LWK][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1228032	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1228034	0.82[AFR][1000 genomes]
rs1228036	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1228038	0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1228039	0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1228040	0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1228042	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1234515	0.82[ASW][hapmap]
rs1234904	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1237924	1.00[EUR][1000 genomes]
rs1238706	1.00[ASW][hapmap];0.88[LWK][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap]
rs1630025	1.00[EUR][1000 genomes]
rs1681623	0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1681624	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1681625	1.00[ASW][hapmap];0.81[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1729286	0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1729287	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs1729288	1.00[ASW][hapmap];0.81[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs1729291	0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2626565	0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2930193	0.95[YRI][hapmap];0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2930194	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2930197	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2950891	1.00[EUR][1000 genomes]
rs73462886	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052397	chr11:47675470-48594256	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv530620	chr11:47765455-48664555	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
3	nsv1036992	chr11:47794621-48666024	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv897326	chr11:47891334-48035474	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1036451	chr11:47902321-48616646	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv541037	chr11:47902321-48616646	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv1047490	chr11:47916708-48388686	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
8	nsv1044266	chr11:47929586-48276132	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv541038	chr11:47929586-48276132	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
10	nsv1053145	chr11:47967902-48086950	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv870381	chr11:47989434-48142648	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
12	esv3396029	chr11:47993857-48241494	Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
13	nsv528641	chr11:48004369-48043053	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv897327	chr11:48004369-48911660	ZNF genes & repeats Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
15	nsv869124	chr11:48014539-48783113	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
16	nsv1051805	chr11:48016488-48378048	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
17	nsv428573	chr11:48032457-48152344	Genic enhancers Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:48018800-48042000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
2	chr11:48025000-48045200	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr11:48026000-48039200	Weak transcription	Fetal Kidney	kidney
4	chr11:48026400-48039200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr11:48027400-48037600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr11:48027400-48044000	Enhancers	Primary T cells fromperipheralblood	blood
7	chr11:48027800-48037600	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr11:48027800-48037800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr11:48027800-48039000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr11:48028000-48038800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr11:48028400-48038800	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr11:48028400-48039200	Weak transcription	Fetal Stomach	stomach
13	chr11:48028600-48035600	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr11:48031800-48041000	Weak transcription	K562	blood
15	chr11:48032400-48038400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
16	chr11:48032400-48042600	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr11:48032400-48045200	Enhancers	Primary B cells from peripheral blood	blood
18	chr11:48032600-48035800	Enhancers	Brain Cingulate Gyrus	brain
19	chr11:48032600-48041200	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr11:48032600-48042800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr11:48032800-48035600	Enhancers	Spleen	Spleen
22	chr11:48032800-48035800	Enhancers	Brain Hippocampus Middle	brain
23	chr11:48032800-48036200	Enhancers	Primary T cells from cord blood	blood
24	chr11:48032800-48042400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr11:48033600-48035600	Enhancers	Brain Anterior Caudate	brain
26	chr11:48033600-48035600	Enhancers	Brain Inferior Temporal Lobe	brain
27	chr11:48033600-48035600	Enhancers	HepG2	liver
28	chr11:48033800-48035600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr11:48033800-48035600	Enhancers	Liver	Liver
30	chr11:48033800-48035600	Enhancers	Brain Substantia Nigra	brain
31	chr11:48033800-48035600	Enhancers	Fetal Thymus	thymus
32	chr11:48033800-48035800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
33	chr11:48033800-48035800	Enhancers	Lung	lung
34	chr11:48033800-48035800	Enhancers	Sigmoid Colon	Sigmoid Colon
35	chr11:48034000-48035600	Enhancers	Fetal Intestine Large	intestine
36	chr11:48034000-48035600	Enhancers	Fetal Muscle Trunk	muscle
37	chr11:48034000-48035800	Enhancers	Duodenum Mucosa	Duodenum
38	chr11:48034000-48035800	Enhancers	Rectal Mucosa Donor 31	rectum
39	chr11:48034000-48040200	Weak transcription	Fetal Heart	heart
40	chr11:48034200-48036200	Enhancers	Primary hematopoietic stem cells	blood
41	chr11:48034200-48038400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr11:48034600-48035600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr11:48034600-48035600	Enhancers	Gastric	stomach
44	chr11:48034600-48035600	Flanking Active TSS	A549	lung
45	chr11:48034600-48035600	Enhancers	Osteobl	bone
46	chr11:48034600-48035800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr11:48034600-48035800	Enhancers	Pancreas	Pancrea
48	chr11:48034600-48035800	Enhancers	Stomach Mucosa	stomach
49	chr11:48034600-48035800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
50	chr11:48034600-48036200	Enhancers	Primary hematopoietic stem cells short term culture	blood

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