Variant report

Variant	rs10876040
Chromosome Location	chr12:50899251-50899252
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:50794531..50796202-chr12:50898772..50900284,2	MCF-7	breast:
2	chr12:50898995..50900548-chr12:50993141..50995760,2	MCF-7	breast:
3	chr12:50897453..50902823-chr12:51156009..51160960,8	MCF-7	breast:
4	chr12:50897525..50900115-chr12:51025935..51031272,7	MCF-7	breast:
5	chr12:50897880..50899909-chr12:51417990..51420226,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000161813	Chromatin interaction
ENSG00000207136	Chromatin interaction
ENSG00000110911	Chromatin interaction
ENSG00000123268	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10083076	1.00[EUR][1000 genomes]
rs10431531	1.00[EUR][1000 genomes]
rs10431532	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10431533	1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10732734	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10747576	1.00[EUR][1000 genomes]
rs10747582	1.00[EUR][1000 genomes]
rs10783355	1.00[EUR][1000 genomes]
rs10783360	1.00[EUR][1000 genomes]
rs10876029	1.00[EUR][1000 genomes]
rs10876079	1.00[EUR][1000 genomes]
rs11169464	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11169472	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs12146806	0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12300290	1.00[EUR][1000 genomes]
rs12302810	0.95[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12302812	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12321891	0.94[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12322925	0.94[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12367373	1.00[EUR][1000 genomes]
rs1464436	1.00[EUR][1000 genomes]
rs1879622	1.00[EUR][1000 genomes]
rs1975351	1.00[EUR][1000 genomes]
rs2037453	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2253376	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2464125	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2468378	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2684895	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2684896	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2684897	1.00[MEX][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2684904	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2684905	1.00[MEX][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2684907	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2684909	1.00[MEX][hapmap];1.00[EUR][1000 genomes]
rs2700476	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2700477	1.00[EUR][1000 genomes]
rs2700481	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2700483	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2731437	1.00[EUR][1000 genomes]
rs2731438	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2731441	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2731444	1.00[MEX][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2731445	1.00[EUR][1000 genomes]
rs2731446	1.00[EUR][1000 genomes]
rs2731447	1.00[MEX][hapmap];1.00[EUR][1000 genomes]
rs2731448	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4238103	1.00[EUR][1000 genomes]
rs4259895	1.00[EUR][1000 genomes]
rs4293196	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4334109	1.00[EUR][1000 genomes]
rs4435082	1.00[EUR][1000 genomes]
rs4477515	1.00[EUR][1000 genomes]
rs4491331	1.00[EUR][1000 genomes]
rs4590959	1.00[EUR][1000 genomes]
rs4617660	1.00[EUR][1000 genomes]
rs4625558	1.00[EUR][1000 genomes]
rs4768854	1.00[EUR][1000 genomes]
rs4768896	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4768897	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4768898	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4768908	1.00[EUR][1000 genomes]
rs4768910	1.00[EUR][1000 genomes]
rs4768916	1.00[EUR][1000 genomes]
rs6421169	1.00[EUR][1000 genomes]
rs6580746	1.00[EUR][1000 genomes]
rs6580749	1.00[EUR][1000 genomes]
rs6580750	1.00[EUR][1000 genomes]
rs6580758	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6580759	0.80[LWK][hapmap];1.00[MEX][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6580762	1.00[EUR][1000 genomes]
rs7133107	1.00[EUR][1000 genomes]
rs7296277	1.00[EUR][1000 genomes]
rs7302222	1.00[EUR][1000 genomes]
rs7304951	1.00[EUR][1000 genomes]
rs7305972	1.00[EUR][1000 genomes]
rs7309410	1.00[EUR][1000 genomes]
rs7309896	1.00[EUR][1000 genomes]
rs7310522	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7310686	1.00[EUR][1000 genomes]
rs7312349	1.00[EUR][1000 genomes]
rs7313783	1.00[EUR][1000 genomes]
rs7314198	1.00[EUR][1000 genomes]
rs7954152	1.00[EUR][1000 genomes]
rs7963866	1.00[EUR][1000 genomes]
rs7964439	1.00[EUR][1000 genomes]
rs7966009	1.00[EUR][1000 genomes]
rs7976281	1.00[MEX][hapmap]
rs939632	1.00[EUR][1000 genomes]
rs939634	1.00[EUR][1000 genomes]
rs9634263	1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9804978	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1820967	chr12:50856613-51002088	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	esv3395665	chr12:50897710-50900258	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50898200-50899400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr12:50898200-50899400	Active TSS	Primary hematopoietic stem cells	blood
3	chr12:50898200-50899400	Active TSS	Hela-S3	cervix
4	chr12:50898200-50899400	Active TSS	HUVEC	blood vessel
5	chr12:50898200-50899600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr12:50898200-50899600	Active TSS	Duodenum Mucosa	Duodenum
7	chr12:50898200-50899600	Active TSS	Rectal Smooth Muscle	rectum
8	chr12:50898200-50899800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr12:50898200-50899800	Active TSS	Fetal Stomach	stomach
10	chr12:50898200-50899800	Active TSS	Rectal Mucosa Donor 31	rectum
11	chr12:50898200-50899800	Active TSS	Osteobl	bone
12	chr12:50898200-50900000	Active TSS	Colonic Mucosa	Colon
13	chr12:50898200-50900000	Active TSS	Fetal Intestine Small	intestine
14	chr12:50898200-50900200	Active TSS	Muscle Satellite Cultured Cells	--
15	chr12:50898200-50900400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr12:50898200-50900400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr12:50898200-50900400	Active TSS	Brain Anterior Caudate	brain
18	chr12:50898200-50900400	Active TSS	Duodenum Smooth Muscle	Duodenum
19	chr12:50898200-50900400	Active TSS	Placenta	Placenta
20	chr12:50898200-50900800	Active TSS	Brain Inferior Temporal Lobe	brain
21	chr12:50898200-50900800	Active TSS	HMEC	breast
22	chr12:50898200-50902200	Active TSS	Brain Angular Gyrus	brain
23	chr12:50898400-50899400	Active TSS	Primary T helper cells fromperipheralblood	blood
24	chr12:50898400-50899600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr12:50898400-50899600	Active TSS	iPS-18 Cell Line	embryonic stem cell
26	chr12:50898400-50899600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr12:50898400-50899600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
28	chr12:50898400-50899600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
29	chr12:50898400-50899600	Active TSS	Colon Smooth Muscle	Colon
30	chr12:50898400-50899600	Active TSS	Fetal Intestine Large	intestine
31	chr12:50898400-50899600	Active TSS	Thymus	Thymus
32	chr12:50898400-50899800	Active TSS	HUES64 Cell Line	embryonic stem cell
33	chr12:50898400-50899800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr12:50898400-50899800	Active TSS	iPS-20b Cell Line	embryonic stem cell
35	chr12:50898400-50899800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr12:50898400-50899800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr12:50898400-50899800	Active TSS	Fetal Brain Male	brain
38	chr12:50898400-50899800	Active TSS	Fetal Heart	heart
39	chr12:50898400-50899800	Active TSS	Lung	lung
40	chr12:50898400-50899800	Active TSS	Placenta Amnion	Placenta Amnion
41	chr12:50898400-50899800	Active TSS	HSMM	muscle
42	chr12:50898400-50899800	Active TSS	NH-A	brain
43	chr12:50898400-50900000	Active TSS	ES-I3 Cell Line	embryonic stem cell
44	chr12:50898400-50900000	Active TSS	HUES48 Cell Line	embryonic stem cell
45	chr12:50898400-50900000	Active TSS	Liver	Liver
46	chr12:50898400-50900000	Active TSS	Esophagus	oesophagus
47	chr12:50898400-50900000	Active TSS	Fetal Lung	lung
48	chr12:50898400-50900000	Active TSS	Pancreas	Pancrea
49	chr12:50898400-50900000	Active TSS	K562	blood
50	chr12:50898400-50900000	Active TSS	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links