Variant report

Variant	rs11229848
Chromosome Location	chr11:58921832-58921833
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:58921112..58922649-chr11:58924123..58926292,2	MCF-7	breast:
2	chr11:58915139..58917844-chr11:58920687..58923095,2	K562	blood:

Variant related genes	Relation type
ENSG00000166801	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10128605	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10128661	0.91[EUR][1000 genomes]
rs10437720	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.92[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10792219	0.88[TSI][hapmap];0.89[EUR][1000 genomes]
rs10792221	0.87[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10896914	0.85[EUR][1000 genomes]
rs10896922	0.89[EUR][1000 genomes]
rs10896924	0.86[CEU][hapmap];0.90[EUR][1000 genomes]
rs10896925	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]
rs10896926	0.90[EUR][1000 genomes]
rs10896928	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10896929	0.94[CEU][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10896930	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10896931	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10896932	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10896933	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10896934	0.89[EUR][1000 genomes]
rs10896935	0.87[EUR][1000 genomes]
rs10896936	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10896937	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10896938	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11229798	0.81[CEU][hapmap];0.86[EUR][1000 genomes]
rs11229799	0.86[EUR][1000 genomes]
rs11229800	0.96[TSI][hapmap];0.87[EUR][1000 genomes]
rs11229801	0.87[EUR][1000 genomes]
rs11229837	0.92[MEX][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11229840	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.92[TSI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11229849	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229850	0.94[CEU][hapmap]
rs11229851	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11229852	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11229854	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11229856	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11823977	0.90[EUR][1000 genomes]
rs11825017	0.90[EUR][1000 genomes]
rs12271831	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12272113	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12274008	0.94[CEU][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12275487	0.94[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12278163	0.93[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12280068	0.94[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12283633	0.93[CEU][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12292185	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12293649	0.94[CEU][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12293695	0.94[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12362905	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12802129	0.90[EUR][1000 genomes]
rs17153379	0.90[EUR][1000 genomes]
rs17153383	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17153415	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1938588	0.90[EUR][1000 genomes]
rs1938589	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1938781	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.92[TSI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2096544	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2096586	0.91[EUR][1000 genomes]
rs2096587	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2105506	0.94[CEU][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2105507	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2154628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2186380	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2282482	0.89[EUR][1000 genomes]
rs2282483	0.88[EUR][1000 genomes]
rs2849739	0.81[EUR][1000 genomes]
rs34027305	0.90[EUR][1000 genomes]
rs34239454	0.86[EUR][1000 genomes]
rs34501069	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35293773	0.86[EUR][1000 genomes]
rs3802961	0.90[EUR][1000 genomes]
rs474847	0.87[EUR][1000 genomes]
rs55657403	0.90[EUR][1000 genomes]
rs55689653	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55989038	0.89[EUR][1000 genomes]
rs56137001	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56239606	0.89[EUR][1000 genomes]
rs58722008	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61902181	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61902223	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7126078	0.90[EUR][1000 genomes]
rs7933787	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7950880	0.87[EUR][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	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	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11229848	FAM111A	cis	parietal	SCAN
rs11229848	OR5AK2	cis	parietal	SCAN
rs11229848	C11orf31	cis	parietal	SCAN
rs11229848	CD5	cis	cerebellum	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:58912800-58924000	Weak transcription	Gastric	stomach
2	chr11:58912800-58924200	Weak transcription	Aorta	Aorta
3	chr11:58912800-58925800	Weak transcription	Ovary	ovary
4	chr11:58913000-58922000	Weak transcription	Psoas Muscle	Psoas
5	chr11:58913000-58922600	Weak transcription	Small Intestine	intestine
6	chr11:58913000-58924600	Weak transcription	Stomach Smooth Muscle	stomach
7	chr11:58913000-58925800	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr11:58913200-58922200	Weak transcription	Fetal Stomach	stomach
9	chr11:58913200-58924400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr11:58913200-58925600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr11:58913200-58925600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr11:58913200-58925800	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr11:58913200-58925800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr11:58913200-58925800	Weak transcription	Brain Anterior Caudate	brain
15	chr11:58913400-58922000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr11:58913400-58922200	Weak transcription	K562	blood
17	chr11:58913600-58922600	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr11:58913800-58922000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr11:58913800-58923800	Weak transcription	Lung	lung
20	chr11:58913800-58925800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr11:58914000-58925800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr11:58914800-58922400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr11:58914800-58922800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr11:58914800-58925800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr11:58915600-58922200	Weak transcription	Fetal Intestine Small	intestine
26	chr11:58916600-58923000	Strong transcription	Primary neutrophils fromperipheralblood	blood
27	chr11:58917600-58925600	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr11:58918000-58925800	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr11:58918200-58922000	Weak transcription	NHDF-Ad	bronchial
30	chr11:58918400-58925800	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr11:58919600-58923400	Weak transcription	Hela-S3	cervix
32	chr11:58919800-58922200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr11:58919800-58924800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr11:58919800-58925600	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr11:58920000-58922200	Weak transcription	Left Ventricle	heart
36	chr11:58920000-58922200	Strong transcription	Thymus	Thymus
37	chr11:58920000-58925600	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr11:58920000-58925600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr11:58920000-58925800	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr11:58920200-58922600	Weak transcription	Fetal Muscle Trunk	muscle
41	chr11:58920200-58925600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr11:58920200-58925600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr11:58920200-58925600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr11:58920200-58925800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr11:58920400-58922000	Weak transcription	HSMM	muscle
46	chr11:58920400-58922200	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr11:58920400-58922400	Weak transcription	NHEK	skin
48	chr11:58920400-58924800	Weak transcription	HUVEC	blood vessel
49	chr11:58920400-58925600	Weak transcription	NHLF	lung
50	chr11:58920400-58925800	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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