Variant report

Variant	rs2041059
Chromosome Location	chr12:1775714-1775715
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:1769849..1773599-chr12:1775643..1780093,7	K562	blood:
2	chr12:1775192..1776787-chr12:1778415..1781197,2	K562	blood:
3	chr12:1751627..1754512-chr12:1774054..1776130,2	MCF-7	breast:
4	chr12:1774006..1776134-chr12:1800067..1801809,2	K562	blood:
5	chr12:1774859..1776787-chr12:1777892..1781197,3	K562	blood:
6	chr12:1774567..1781960-chr12:1797936..1801472,7	MCF-7	breast:
7	chr12:1774139..1776041-chr12:1794972..1797098,2	MCF-7	breast:
8	chr12:1769488..1776078-chr12:1798561..1806450,20	K562	blood:

No data

Variant related genes	Relation type
ENSG00000111186	Chromatin interaction
ENSG00000006831	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10744546	0.87[AFR][1000 genomes]
rs11061904	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1860049	1.00[EUR][1000 genomes]
rs2108398	1.00[EUR][1000 genomes]
rs2369974	1.00[EUR][1000 genomes]
rs2370054	1.00[EUR][1000 genomes]
rs35510932	1.00[EUR][1000 genomes]
rs4765838	1.00[EUR][1000 genomes]
rs4766411	0.83[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4766420	1.00[EUR][1000 genomes]
rs56369812	1.00[EUR][1000 genomes]
rs6489321	1.00[EUR][1000 genomes]
rs6489325	1.00[EUR][1000 genomes]
rs7133749	1.00[EUR][1000 genomes]
rs7135229	1.00[EUR][1000 genomes]
rs7297878	1.00[EUR][1000 genomes]
rs7304843	1.00[EUR][1000 genomes]
rs7308757	1.00[EUR][1000 genomes]
rs7314133	1.00[EUR][1000 genomes]
rs74061311	1.00[EUR][1000 genomes]
rs74061331	1.00[EUR][1000 genomes]
rs74061332	1.00[EUR][1000 genomes]
rs758026	1.00[EUR][1000 genomes]
rs758027	1.00[EUR][1000 genomes]
rs758169	1.00[EUR][1000 genomes]
rs7957003	1.00[EUR][1000 genomes]
rs7962777	1.00[EUR][1000 genomes]
rs7964434	1.00[EUR][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	nsv1042863	chr12:1163817-1902302	Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv541345	chr12:1163817-1902302	Strong transcription Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv898584	chr12:1607390-1783251	Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv832304	chr12:1710249-1868642	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats 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	24 gene(s)	inside rSNPs	diseases
5	nsv832305	chr12:1769852-1936054	Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:1771400-1775800	Weak transcription	Brain Angular Gyrus	brain
2	chr12:1771400-1775800	Weak transcription	Brain Hippocampus Middle	brain
3	chr12:1771400-1775800	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr12:1771400-1776000	Weak transcription	Brain Anterior Caudate	brain
5	chr12:1771400-1776000	Weak transcription	Brain Cingulate Gyrus	brain
6	chr12:1771400-1777600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr12:1771400-1777800	Weak transcription	GM12878-XiMat	blood
8	chr12:1771600-1776000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr12:1771600-1776000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr12:1771600-1776000	Weak transcription	Ovary	ovary
11	chr12:1771600-1778000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr12:1772200-1776200	Weak transcription	Primary B cells from peripheral blood	blood
13	chr12:1772200-1778000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr12:1772400-1775800	Weak transcription	Fetal Brain Female	brain
15	chr12:1772400-1776000	Weak transcription	Fetal Brain Male	brain
16	chr12:1772400-1776200	Weak transcription	Colonic Mucosa	Colon
17	chr12:1772600-1776000	Weak transcription	Pancreas	Pancrea
18	chr12:1772600-1776200	Weak transcription	Left Ventricle	heart
19	chr12:1772600-1776200	Weak transcription	Right Atrium	heart
20	chr12:1772600-1778200	Weak transcription	Lung	lung
21	chr12:1772800-1776200	Weak transcription	Spleen	Spleen
22	chr12:1772800-1776400	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr12:1773400-1776000	Weak transcription	Right Ventricle	heart
24	chr12:1773800-1778600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
25	chr12:1774000-1777000	Enhancers	Fetal Intestine Large	intestine
26	chr12:1774000-1778000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr12:1774000-1778200	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr12:1774200-1776600	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr12:1774200-1776600	Enhancers	A549	lung
30	chr12:1774200-1778000	Enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr12:1774400-1776000	Weak transcription	Small Intestine	intestine
32	chr12:1774400-1778200	Enhancers	Primary T killer memory cells from peripheral blood	blood
33	chr12:1774400-1778200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr12:1774600-1775800	Weak transcription	Brain Substantia Nigra	brain
35	chr12:1774600-1776000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr12:1774600-1776000	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr12:1774600-1776200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr12:1774600-1777600	Weak transcription	Thymus	Thymus
39	chr12:1774600-1777800	Weak transcription	Hela-S3	cervix
40	chr12:1774800-1775800	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr12:1774800-1776000	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr12:1775000-1776400	Enhancers	Primary T cells from cord blood	blood
43	chr12:1775200-1775800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
44	chr12:1775200-1776000	Enhancers	Duodenum Mucosa	Duodenum
45	chr12:1775200-1776000	Enhancers	Rectal Mucosa Donor 31	rectum
46	chr12:1775200-1776600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
47	chr12:1775200-1776800	Enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr12:1775200-1777200	Enhancers	Adipose Nuclei	Adipose
49	chr12:1775200-1778200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
50	chr12:1775200-1778400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links