Variant report

Variant	rs10896924
Chromosome Location	chr11:58889191-58889192
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:58872425..58874544-chr11:58888169..58890358,2	MCF-7	breast:
2	chr11:58884380..58886693-chr11:58887312..58889287,2	K562	blood:

Extended variants
information (count: 97 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10128559	0.92[ASN][1000 genomes]
rs10128605	0.80[EUR][1000 genomes]
rs10128661	0.88[EUR][1000 genomes]
rs10437720	0.93[CEU][hapmap];0.97[EUR][1000 genomes]
rs10792219	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10792221	0.91[CEU][hapmap];0.94[EUR][1000 genomes]
rs10896914	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10896922	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10896925	0.93[CEU][hapmap];0.97[EUR][1000 genomes]
rs10896926	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10896928	0.93[CEU][hapmap];0.94[EUR][1000 genomes]
rs10896929	0.93[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10896930	0.94[EUR][1000 genomes]
rs10896931	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[EUR][1000 genomes]
rs10896932	0.89[CHB][hapmap];0.94[EUR][1000 genomes]
rs10896933	0.93[EUR][1000 genomes]
rs10896934	0.86[EUR][1000 genomes]
rs10896935	0.84[EUR][1000 genomes]
rs10896936	0.93[EUR][1000 genomes]
rs10896937	0.93[EUR][1000 genomes]
rs10896938	0.85[EUR][1000 genomes]
rs10896947	0.93[CEU][hapmap]
rs11229795	0.92[ASN][1000 genomes]
rs11229798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11229799	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11229800	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11229801	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11229837	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11229840	0.93[CEU][hapmap];0.93[EUR][1000 genomes]
rs11229848	0.86[CEU][hapmap];0.90[EUR][1000 genomes]
rs11229849	0.93[CEU][hapmap];0.94[EUR][1000 genomes]
rs11229850	0.93[CEU][hapmap];1.00[CHB][hapmap]
rs11229851	0.94[EUR][1000 genomes]
rs11229852	0.94[EUR][1000 genomes]
rs11229854	0.94[EUR][1000 genomes]
rs11229856	0.93[EUR][1000 genomes]
rs11823977	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11825017	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12271831	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[EUR][1000 genomes]
rs12272113	0.94[EUR][1000 genomes]
rs12274008	0.93[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes]
rs12275487	0.93[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes]
rs12278163	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes]
rs12280068	0.93[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes]
rs12283633	0.92[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12292185	0.91[EUR][1000 genomes]
rs12293649	0.93[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes]
rs12293695	0.93[CEU][hapmap];0.94[EUR][1000 genomes]
rs12362905	0.94[EUR][1000 genomes]
rs12802129	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17153379	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17153383	0.97[EUR][1000 genomes]
rs17153415	0.90[EUR][1000 genomes]
rs1938588	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1938589	0.97[EUR][1000 genomes]
rs1938781	0.93[CEU][hapmap];0.94[EUR][1000 genomes]
rs1943146	0.89[ASN][1000 genomes]
rs1943147	0.89[ASN][1000 genomes]
rs2096544	0.94[EUR][1000 genomes]
rs2096586	0.88[EUR][1000 genomes]
rs2096587	0.91[EUR][1000 genomes]
rs2105506	0.93[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2105507	0.94[EUR][1000 genomes]
rs2154628	0.86[CEU][hapmap];0.86[EUR][1000 genomes]
rs2186380	0.91[CEU][hapmap];0.94[EUR][1000 genomes]
rs2282482	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2282483	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2839968	0.93[CEU][hapmap]
rs2844342	0.90[ASN][1000 genomes]
rs2849739	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34027305	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34239454	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34501069	0.94[EUR][1000 genomes]
rs35293773	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3802961	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs474847	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs530386	0.84[ASN][1000 genomes]
rs55657403	0.87[EUR][1000 genomes]
rs55689653	0.94[EUR][1000 genomes]
rs55989038	0.86[EUR][1000 genomes]
rs56137001	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56239606	0.86[EUR][1000 genomes]
rs58722008	0.89[EUR][1000 genomes]
rs61902181	0.94[EUR][1000 genomes]
rs61902223	0.94[EUR][1000 genomes]
rs7126078	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7933787	0.93[CEU][hapmap];0.94[EUR][1000 genomes]
rs7950880	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][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

No data

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	chr11:58884000-58890800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr11:58884000-58894800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr11:58885200-58891600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr11:58886000-58898800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr11:58886400-58893600	Strong transcription	Fetal Thymus	thymus
12	chr11:58886600-58890800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr11:58886600-58898600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr11:58886800-58889200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr11:58886800-58889800	Weak transcription	Fetal Stomach	stomach
16	chr11:58886800-58890800	Weak transcription	HSMM	muscle
17	chr11:58886800-58892000	Weak transcription	NHDF-Ad	bronchial
18	chr11:58886800-58893400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr11:58886800-58898400	Weak transcription	Osteobl	bone
20	chr11:58886800-58898800	Weak transcription	Rectal Smooth Muscle	rectum
21	chr11:58886800-58901200	Weak transcription	NHLF	lung
22	chr11:58886800-58903400	Weak transcription	NHEK	skin
23	chr11:58887000-58889200	Weak transcription	NH-A	brain
24	chr11:58887000-58890000	Weak transcription	Thymus	Thymus
25	chr11:58887000-58890600	Weak transcription	Fetal Lung	lung
26	chr11:58887000-58890800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr11:58887000-58890800	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr11:58887000-58891000	Weak transcription	Duodenum Mucosa	Duodenum
29	chr11:58887000-58891200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr11:58887000-58891600	Weak transcription	HMEC	breast
31	chr11:58887000-58891600	Weak transcription	HUVEC	blood vessel
32	chr11:58887000-58891800	Weak transcription	Primary B cells from cord blood	blood
33	chr11:58887000-58891800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr11:58887000-58892000	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr11:58887000-58892800	Weak transcription	Fetal Intestine Large	intestine
36	chr11:58887000-58899000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr11:58887000-58899000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr11:58887200-58891600	Weak transcription	Primary B cells from peripheral blood	blood
39	chr11:58887800-58891000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr11:58887800-58894600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
41	chr11:58888200-58890000	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr11:58888200-58890400	Strong transcription	H1 Cell Line	embryonic stem cell
43	chr11:58888200-58891600	Weak transcription	Fetal Kidney	kidney
44	chr11:58888200-58893800	Weak transcription	HepG2	liver
45	chr11:58888400-58890000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr11:58888400-58890200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr11:58888400-58890200	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr11:58888400-58890800	Weak transcription	Primary hematopoietic stem cells	blood
49	chr11:58888400-58891200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr11:58888400-58891600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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