Variant report

Variant	rs2559644
Chromosome Location	chr12:105035001-105035002
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	chr12:105034278..105037012-chr12:105037513..105039770,2	MCF-7	breast:

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10861261	0.87[ASN][1000 genomes]
rs11112143	0.87[ASN][1000 genomes]
rs11112144	0.84[ASN][1000 genomes]
rs17815142	0.92[ASN][1000 genomes]
rs1863879	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2559638	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2694409	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2694410	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2694411	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2694412	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2694413	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2694415	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2694416	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2695997	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2695998	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2695999	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2696000	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2696001	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2696002	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs703658	0.83[EUR][1000 genomes]
rs727862	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899495	chr12:104990469-105527011	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1050695	chr12:105000981-105125161	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv541589	chr12:105000981-105125161	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105013800-105037000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr12:105017000-105036000	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr12:105020800-105037800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr12:105021000-105037800	Weak transcription	NHEK	skin
5	chr12:105022400-105048200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr12:105022800-105043200	Weak transcription	Brain Hippocampus Middle	brain
7	chr12:105023000-105036800	Weak transcription	Primary T cells from cord blood	blood
8	chr12:105024600-105044200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr12:105024800-105038200	Weak transcription	Brain Cingulate Gyrus	brain
10	chr12:105026800-105036800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr12:105027600-105038000	Weak transcription	Colonic Mucosa	Colon
12	chr12:105027800-105037800	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr12:105030400-105037400	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr12:105030600-105036600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr12:105030600-105037400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr12:105030800-105037200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr12:105031800-105036800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr12:105031800-105037000	Weak transcription	K562	blood
19	chr12:105031800-105038400	Weak transcription	Brain Anterior Caudate	brain
20	chr12:105032000-105036800	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr12:105032400-105036800	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr12:105032400-105037200	Weak transcription	Duodenum Mucosa	Duodenum
23	chr12:105032400-105037800	Weak transcription	Gastric	stomach
24	chr12:105032400-105037800	Weak transcription	Stomach Smooth Muscle	stomach
25	chr12:105032600-105035600	ZNF genes & repeats	GM12878-XiMat	blood
26	chr12:105032800-105035200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr12:105032800-105035200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr12:105032800-105036800	Enhancers	Monocytes-CD14+_RO01746	blood
29	chr12:105032800-105038000	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr12:105033000-105050200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr12:105033200-105035200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
32	chr12:105033200-105035200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
33	chr12:105033200-105036400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr12:105033400-105037600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr12:105033400-105038200	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr12:105033400-105050200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr12:105033600-105035400	ZNF genes & repeats	Primary B cells from peripheral blood	blood
38	chr12:105033600-105036200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr12:105033600-105037800	Weak transcription	Right Ventricle	heart
40	chr12:105033600-105038200	Weak transcription	Left Ventricle	heart
41	chr12:105033600-105040600	Weak transcription	A549	lung
42	chr12:105033600-105050200	Weak transcription	Right Atrium	heart
43	chr12:105034000-105035200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr12:105034400-105035200	ZNF genes & repeats	Thymus	Thymus
45	chr12:105034600-105035200	Enhancers	Primary neutrophils fromperipheralblood	blood
46	chr12:105034600-105035400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr12:105034600-105035400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
48	chr12:105034800-105035800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr12:105034800-105036000	Genic enhancers	Dnd41	blood
50	chr12:105035000-105035200	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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