Variant report

Variant	rs10896925
Chromosome Location	chr11:58891292-58891293
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:58890846..58893267-chr11:58894892..58896437,2	MCF-7	breast:

Extended variants
information (count: 90 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10128605	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10128661	0.85[EUR][1000 genomes]
rs10437720	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10792219	0.95[CEU][hapmap];0.96[TSI][hapmap];0.95[EUR][1000 genomes]
rs10792221	0.93[CEU][hapmap];0.87[CHB][hapmap];0.92[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10896914	0.91[EUR][1000 genomes]
rs10896922	0.95[CEU][hapmap];0.95[EUR][1000 genomes]
rs10896924	0.93[CEU][hapmap];0.97[EUR][1000 genomes]
rs10896926	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs10896928	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10896929	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10896930	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10896931	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10896932	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10896933	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10896934	0.84[EUR][1000 genomes]
rs10896935	0.81[EUR][1000 genomes]
rs10896936	0.90[EUR][1000 genomes]
rs10896937	0.90[EUR][1000 genomes]
rs10896938	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10896947	0.89[CEU][hapmap]
rs11229798	0.94[CEU][hapmap];0.92[EUR][1000 genomes]
rs11229799	0.83[CEU][hapmap];0.93[EUR][1000 genomes]
rs11229800	0.94[CEU][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes]
rs11229801	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11229837	0.95[CEU][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs11229840	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11229848	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.92[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11229849	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11229851	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11229852	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11229854	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11229856	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11823977	0.97[EUR][1000 genomes]
rs11825017	0.97[EUR][1000 genomes]
rs12271831	0.95[CEU][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12272113	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12274008	0.92[MEX][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12275487	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12278163	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12280068	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12283633	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12292185	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12293649	0.92[MEX][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12293695	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12362905	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12802129	0.97[EUR][1000 genomes]
rs17153379	0.97[EUR][1000 genomes]
rs17153383	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17153415	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1938588	0.97[EUR][1000 genomes]
rs1938589	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1938781	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2096544	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2096586	0.85[EUR][1000 genomes]
rs2096587	0.88[EUR][1000 genomes]
rs2105506	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2105507	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2154628	1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2186380	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2282482	0.95[EUR][1000 genomes]
rs2282483	0.94[EUR][1000 genomes]
rs2839968	0.89[CEU][hapmap]
rs2849739	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34027305	0.91[EUR][1000 genomes]
rs34239454	0.93[EUR][1000 genomes]
rs34501069	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35293773	0.93[EUR][1000 genomes]
rs3802961	0.97[EUR][1000 genomes]
rs474847	0.92[EUR][1000 genomes]
rs55657403	0.84[EUR][1000 genomes]
rs55689653	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55989038	0.83[EUR][1000 genomes]
rs56137001	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56239606	0.84[EUR][1000 genomes]
rs58722008	0.86[EUR][1000 genomes]
rs61902181	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61902223	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7126078	0.97[EUR][1000 genomes]
rs7933787	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7950880	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050013	chr11:58394598-59221090	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv948365	chr11:58515163-59156405	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	esv2758272	chr11:58700092-59008673	Bivalent/Poised TSS Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv2759830	chr11:58700092-59008673	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
5	esv2757447	chr11:58746238-58906018	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
6	nsv975329	chr11:58767290-58907813	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv430388	chr11:58769524-58925824	Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
8	nsv468578	chr11:58790628-58901763	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv555147	chr11:58790628-58901763	Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10896925	CD5	cis	cerebellum	SCAN
rs10896925	OR5AK2	cis	parietal	SCAN
rs10896925	C11orf31	cis	parietal	SCAN
rs10896925	OR1S2	cis	parietal	SCAN
rs10896925	FAM111A	cis	parietal	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:58875200-58909600	Weak transcription	Stomach Mucosa	stomach
2	chr11:58875400-58909600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr11:58876200-58891800	Weak transcription	Fetal Heart	heart
4	chr11:58876200-58892000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr11:58880800-58894800	ZNF genes & repeats	Dnd41	blood
6	chr11:58881600-58903600	Weak transcription	Hela-S3	cervix
7	chr11:58884000-58894800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr11:58885200-58891600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr11:58886000-58898800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr11:58886400-58893600	Strong transcription	Fetal Thymus	thymus
11	chr11:58886600-58898600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr11:58886800-58892000	Weak transcription	NHDF-Ad	bronchial
13	chr11:58886800-58893400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr11:58886800-58898400	Weak transcription	Osteobl	bone
15	chr11:58886800-58898800	Weak transcription	Rectal Smooth Muscle	rectum
16	chr11:58886800-58901200	Weak transcription	NHLF	lung
17	chr11:58886800-58903400	Weak transcription	NHEK	skin
18	chr11:58887000-58891600	Weak transcription	HMEC	breast
19	chr11:58887000-58891600	Weak transcription	HUVEC	blood vessel
20	chr11:58887000-58891800	Weak transcription	Primary B cells from cord blood	blood
21	chr11:58887000-58891800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr11:58887000-58892000	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr11:58887000-58892800	Weak transcription	Fetal Intestine Large	intestine
24	chr11:58887000-58899000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr11:58887000-58899000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr11:58887200-58891600	Weak transcription	Primary B cells from peripheral blood	blood
27	chr11:58887800-58894600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
28	chr11:58888200-58891600	Weak transcription	Fetal Kidney	kidney
29	chr11:58888200-58893800	Weak transcription	HepG2	liver
30	chr11:58888400-58891600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr11:58888400-58891600	Weak transcription	Fetal Muscle Leg	muscle
32	chr11:58888400-58892200	Strong transcription	A549	lung
33	chr11:58888400-58899400	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr11:58889800-58894600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
35	chr11:58890000-58893000	Weak transcription	Fetal Brain Male	brain
36	chr11:58890000-58893600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr11:58890000-58894600	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
38	chr11:58890200-58894200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr11:58890400-58891600	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr11:58890600-58892000	Strong transcription	Fetal Lung	lung
41	chr11:58890600-58894400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
42	chr11:58890800-58892200	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr11:58890800-58892800	Strong transcription	Primary hematopoietic stem cells	blood
44	chr11:58890800-58893200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr11:58890800-58893600	Strong transcription	HSMM	muscle
46	chr11:58890800-58893800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr11:58890800-58893800	ZNF genes & repeats	GM12878-XiMat	blood
48	chr11:58890800-58893800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
49	chr11:58890800-58894000	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr11:58890800-58894400	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links