Variant report

Variant	rs2820216
Chromosome Location	chr6:53778865-53778866
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:53658853..53661753-chr6:53777848..53780976,4	MCF-7	breast:
2	chr6:53778649..53781585-chr6:53788522..53790145,2	MCF-7	breast:
3	chr6:53774348..53776830-chr6:53777789..53780459,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228614	Chromatin interaction
ENSG00000137269	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10948779	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13220665	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap]
rs2745461	0.86[EUR][1000 genomes]
rs2745462	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2820215	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3000996	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3000997	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3000999	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3001000	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3001001	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3001002	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3001009	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3001010	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3003489	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3003491	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3003493	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs3003500	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3003501	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34861916	0.81[AMR][1000 genomes]
rs35389351	0.81[AMR][1000 genomes]
rs3813849	0.90[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.94[YRI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4236113	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4236115	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4265033	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4276502	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4286781	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4321822	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4326237	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4336450	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4351263	1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4382260	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4398733	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4437471	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4484515	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4489155	0.90[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.80[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.94[YRI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4591854	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4613824	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4615391	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4712048	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4712049	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4715424	0.94[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4715426	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6458957	0.87[EUR][1000 genomes]
rs6458958	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6458959	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6458961	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6458962	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6458965	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6458966	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6458969	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6458971	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6458972	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6650996	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6901644	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6920743	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6924025	0.93[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6926478	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6937901	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs742524	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes]
rs7739965	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7753504	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7754791	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7759946	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs7762883	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7763081	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7763147	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7769893	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7774173	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9296719	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9296721	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9367544	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9370235	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9370239	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9382234	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[YRI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9382237	0.87[EUR][1000 genomes]
rs9382250	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9395886	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9474694	1.00[CHB][hapmap]

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	nsv1034955	chr6:53447607-53931055	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv830664	chr6:53698021-53825270	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53752800-53782000	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr6:53754800-53779800	Weak transcription	NHLF	lung
3	chr6:53755000-53779800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr6:53756000-53781800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr6:53759200-53787600	Weak transcription	Spleen	Spleen
6	chr6:53759200-53794400	Weak transcription	Right Ventricle	heart
7	chr6:53759400-53786400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr6:53759600-53789800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr6:53760400-53789400	Weak transcription	Stomach Mucosa	stomach
10	chr6:53760400-53791200	Weak transcription	Hela-S3	cervix
11	chr6:53760600-53793600	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr6:53761000-53782000	Weak transcription	Fetal Kidney	kidney
13	chr6:53761000-53782800	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr6:53761000-53785400	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr6:53761400-53787400	Weak transcription	HMEC	breast
16	chr6:53761400-53791200	Weak transcription	Colon Smooth Muscle	Colon
17	chr6:53761600-53790800	Weak transcription	Fetal Heart	heart
18	chr6:53761800-53786800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr6:53762000-53791200	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr6:53762000-53791600	Weak transcription	Fetal Lung	lung
21	chr6:53762200-53786800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr6:53764400-53784600	Weak transcription	Primary hematopoietic stem cells	blood
23	chr6:53768600-53785000	Weak transcription	Primary B cells from cord blood	blood
24	chr6:53768800-53796000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr6:53769000-53785400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr6:53769200-53790400	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr6:53769600-53785200	Weak transcription	Rectal Smooth Muscle	rectum
28	chr6:53769800-53779000	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr6:53769800-53784400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr6:53769800-53784400	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr6:53770000-53781800	Weak transcription	HSMM	muscle
32	chr6:53770000-53782000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr6:53770000-53795800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr6:53770600-53787400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr6:53771200-53785000	Weak transcription	Left Ventricle	heart
36	chr6:53771800-53779000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr6:53772000-53784200	Weak transcription	Colonic Mucosa	Colon
38	chr6:53772000-53784400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr6:53772000-53787600	Weak transcription	Pancreas	Pancrea
40	chr6:53772000-53803000	Weak transcription	Lung	lung
41	chr6:53772800-53783800	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr6:53775800-53781200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr6:53776000-53786600	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr6:53776000-53790600	Weak transcription	Brain Germinal Matrix	brain
45	chr6:53776200-53786400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr6:53776400-53786600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr6:53776600-53785200	Weak transcription	Ovary	ovary
48	chr6:53776600-53789200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr6:53776800-53791000	Weak transcription	HUVEC	blood vessel
50	chr6:53777000-53781600	Weak transcription	Brain Angular Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links