Variant report

Variant	rs11005621
Chromosome Location	chr10:52186223-52186224
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:52184358..52187257-chr10:52191960..52194304,3	K562	blood:
2	chr10:52186220..52188065-chr10:52229199..52231914,2	MCF-7	breast:
3	chr10:52185055..52188816-chr10:52196257..52198755,3	MCF-7	breast:

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10458673	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10508927	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10508928	0.84[CEU][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10508929	0.97[ASN][1000 genomes]
rs10740684	0.97[ASN][1000 genomes]
rs10763365	0.82[EUR][1000 genomes]
rs10763373	0.84[CEU][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10763382	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10763426	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10763500	0.89[ASN][1000 genomes]
rs10825789	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs10825825	0.86[EUR][1000 genomes]
rs10825859	0.92[ASN][1000 genomes]
rs10825861	0.91[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10825882	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10825904	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10825934	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10825978	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10825995	0.93[ASN][1000 genomes]
rs10825996	0.93[ASN][1000 genomes]
rs10826013	0.93[ASN][1000 genomes]
rs10826033	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10826036	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10826169	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs11005356	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11005399	0.84[CEU][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11005415	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11005418	0.92[CEU][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11005579	0.88[CEU][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11005614	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11005761	0.91[ASN][1000 genomes]
rs11005803	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11005884	0.89[ASN][1000 genomes]
rs11006054	0.81[AMR][1000 genomes]
rs12217648	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12219070	0.90[ASN][1000 genomes]
rs12219692	0.90[AFR][1000 genomes]
rs1884572	1.00[CEU][hapmap];0.86[ASN][1000 genomes]
rs1916572	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2024872	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2144863	0.86[ASN][1000 genomes]
rs2273402	0.87[ASN][1000 genomes]
rs2339503	0.88[ASN][1000 genomes]
rs2339507	0.86[ASN][1000 genomes]
rs34122137	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3739989	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4519042	0.81[AFR][1000 genomes]
rs4935165	0.89[ASN][1000 genomes]
rs4935711	0.87[ASN][1000 genomes]
rs4935728	0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs7079881	0.85[ASN][1000 genomes]
rs7086029	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7090807	0.89[ASN][1000 genomes]
rs7092749	0.84[CEU][hapmap];0.88[EUR][1000 genomes]
rs768185	0.84[CEU][hapmap];0.88[EUR][1000 genomes]
rs7896315	0.87[ASN][1000 genomes]
rs7904375	0.84[EUR][1000 genomes]
rs7920818	1.00[CEU][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7922802	0.84[CEU][hapmap]
rs910817	0.85[ASN][1000 genomes]
rs927047	0.85[ASN][1000 genomes]
rs927048	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs9919413	0.80[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054775	chr10:51595893-52392361	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers 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 target site	43 gene(s)	inside rSNPs	diseases
2	nsv1051087	chr10:51886486-52447295	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv916214	chr10:51886486-52458983	Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv918212	chr10:51886486-52465482	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv817412	chr10:51911034-52432990	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking 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 target site	31 gene(s)	inside rSNPs	diseases
6	nsv521273	chr10:52051645-52197847	Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52178400-52220000	Weak transcription	Pancreas	Pancrea
2	chr10:52178600-52188800	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr10:52178600-52217200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr10:52178600-52219400	Weak transcription	Left Ventricle	heart
5	chr10:52178800-52187400	Weak transcription	Primary T cells from cord blood	blood
6	chr10:52178800-52191200	Weak transcription	HSMMtube	muscle
7	chr10:52178800-52198000	Weak transcription	Fetal Thymus	thymus
8	chr10:52178800-52202800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr10:52179000-52191000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr10:52179000-52191200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr10:52179000-52191400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr10:52179000-52191600	Weak transcription	Duodenum Mucosa	Duodenum
13	chr10:52179000-52205800	Weak transcription	Primary hematopoietic stem cells	blood
14	chr10:52179000-52207600	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr10:52179000-52209000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr10:52179200-52196600	Weak transcription	Colon Smooth Muscle	Colon
17	chr10:52180000-52189800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr10:52180000-52190800	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr10:52180200-52201200	Weak transcription	Fetal Heart	heart
20	chr10:52180600-52194000	Weak transcription	Fetal Intestine Large	intestine
21	chr10:52181400-52191000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr10:52181600-52187200	Weak transcription	K562	blood
23	chr10:52181600-52187800	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr10:52181600-52189800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr10:52181600-52190800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr10:52181600-52219400	Weak transcription	Placenta	Placenta
27	chr10:52181800-52206200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr10:52182000-52191200	Weak transcription	Primary B cells from peripheral blood	blood
29	chr10:52182200-52191000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr10:52182200-52191400	Weak transcription	Psoas Muscle	Psoas
31	chr10:52182200-52220000	Weak transcription	Fetal Stomach	stomach
32	chr10:52182400-52189800	Weak transcription	Adipose Nuclei	Adipose
33	chr10:52182600-52191000	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr10:52182600-52191000	Weak transcription	Fetal Lung	lung
35	chr10:52182600-52200600	Weak transcription	Fetal Brain Male	brain
36	chr10:52183000-52191200	Weak transcription	Brain Angular Gyrus	brain
37	chr10:52183200-52189600	Weak transcription	Brain Substantia Nigra	brain
38	chr10:52183400-52190000	Weak transcription	Brain Hippocampus Middle	brain
39	chr10:52183400-52190600	Weak transcription	Brain Cingulate Gyrus	brain
40	chr10:52183400-52191400	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr10:52184000-52189600	Weak transcription	Brain Anterior Caudate	brain
42	chr10:52184000-52191200	Weak transcription	Liver	Liver
43	chr10:52184200-52189800	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr10:52184200-52191400	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr10:52184400-52191200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr10:52185600-52191600	Weak transcription	Primary B cells from cord blood	blood
47	chr10:52186200-52186600	Enhancers	Primary monocytes fromperipheralblood	blood
48	chr10:52186200-52186600	Enhancers	Primary hematopoietic stem cells short term culture	blood
49	chr10:52186200-52186600	Flanking Active TSS	GM12878-XiMat	blood
50	chr10:52186200-52186600	Enhancers	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links