Variant report

Variant	rs1740761
Chromosome Location	chr10:52219553-52219554
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	chr10:52218961..52222149-chr10:52229280..52232143,4	MCF-7	breast:

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10508931	0.86[CHB][hapmap]
rs11006190	0.86[CHB][hapmap]
rs11006191	0.86[CHB][hapmap]
rs11006193	0.86[CHB][hapmap]
rs11006194	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs11006197	0.86[CHB][hapmap]
rs11006200	0.86[CHB][hapmap]
rs11006213	0.86[CHB][hapmap]
rs11006233	0.86[CHB][hapmap]
rs11006237	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs11006238	0.86[CHB][hapmap]
rs1203375	0.85[ASN][1000 genomes]
rs1203382	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1203386	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1203390	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1203393	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1203394	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1203395	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1203401	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1203403	1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1203405	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1203407	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1203409	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1203410	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1203411	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1203413	0.80[CEU][hapmap]
rs1203415	0.82[CEU][hapmap]
rs1203418	0.85[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs1203420	0.91[ASN][1000 genomes]
rs1203421	0.86[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs17496403	0.86[CHB][hapmap]
rs17496500	0.86[CHB][hapmap]
rs1810576	0.98[ASN][1000 genomes]
rs1916567	0.86[CEU][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs2221	0.95[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2339402	0.90[ASN][1000 genomes]
rs2574985	0.80[CEU][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs2983347	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2983350	0.94[CEU][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2983354	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2983357	0.95[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2983359	0.95[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2983361	0.95[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2983368	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2983369	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2983370	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2983371	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3011770	0.90[CEU][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3011771	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3011773	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3011779	0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs3011780	0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs3011782	0.91[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3011783	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3011786	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3011787	1.00[CEU][hapmap];0.86[JPT][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3011788	0.95[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3011789	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3011790	0.95[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap];0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3011791	0.95[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3011792	0.95[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3011793	0.85[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3011794	0.95[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3011797	0.95[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3011801	0.95[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4312019	0.80[CEU][hapmap]
rs7072826	0.86[CHB][hapmap]
rs7921226	0.86[CHB][hapmap]
rs920136	0.92[JPT][hapmap];0.87[ASN][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	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

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52178400-52220000	Weak transcription	Pancreas	Pancrea
2	chr10:52182200-52220000	Weak transcription	Fetal Stomach	stomach
3	chr10:52191800-52219600	Weak transcription	Fetal Lung	lung
4	chr10:52192000-52219600	Weak transcription	Adipose Nuclei	Adipose
5	chr10:52192400-52219600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr10:52192400-52219600	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr10:52192400-52220000	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr10:52192400-52229400	Weak transcription	Aorta	Aorta
9	chr10:52192400-52230400	Weak transcription	HSMM	muscle
10	chr10:52197800-52229800	Weak transcription	Gastric	stomach
11	chr10:52204400-52228600	Weak transcription	NHDF-Ad	bronchial
12	chr10:52206600-52219600	Weak transcription	Fetal Intestine Large	intestine
13	chr10:52207800-52219600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr10:52207800-52220000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr10:52207800-52221800	Weak transcription	Psoas Muscle	Psoas
16	chr10:52208000-52219600	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr10:52208000-52219600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr10:52208000-52219600	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr10:52208000-52219600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr10:52208000-52219600	Weak transcription	Thymus	Thymus
21	chr10:52208000-52240200	Weak transcription	Esophagus	oesophagus
22	chr10:52208200-52229600	Weak transcription	Right Ventricle	heart
23	chr10:52208400-52230400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr10:52209600-52220000	Weak transcription	Spleen	Spleen
25	chr10:52209600-52229200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr10:52209800-52219800	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr10:52211600-52219600	Weak transcription	Brain Cingulate Gyrus	brain
28	chr10:52211600-52223800	Weak transcription	Colon Smooth Muscle	Colon
29	chr10:52211800-52229400	Weak transcription	NHEK	skin
30	chr10:52212600-52219600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr10:52212800-52219600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr10:52212800-52219600	Weak transcription	Brain Substantia Nigra	brain
33	chr10:52212800-52229400	Weak transcription	Primary hematopoietic stem cells	blood
34	chr10:52212800-52229600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr10:52214200-52219800	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr10:52215000-52219600	Weak transcription	Fetal Heart	heart
37	chr10:52215000-52230400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr10:52215200-52228800	Weak transcription	HepG2	liver
39	chr10:52215200-52229000	Weak transcription	Brain Angular Gyrus	brain
40	chr10:52215400-52219800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr10:52215400-52220000	Weak transcription	Lung	lung
42	chr10:52215600-52228600	Weak transcription	HSMMtube	muscle
43	chr10:52215800-52228600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr10:52216000-52219600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr10:52216000-52221600	Weak transcription	Stomach Smooth Muscle	stomach
46	chr10:52216200-52219600	Weak transcription	Primary B cells from cord blood	blood
47	chr10:52216200-52219600	Weak transcription	Duodenum Mucosa	Duodenum
48	chr10:52216400-52219600	Weak transcription	Fetal Thymus	thymus
49	chr10:52216400-52228600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr10:52216800-52219600	Weak transcription	K562	blood

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