Variant report

Variant	rs10838681
Chromosome Location	chr11:47275064-47275065
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYBL2	chr11:47275035-47275530	HepG2	liver:	n/a	n/a
2	POLR2A	chr11:47275052-47275745	HepG2	liver:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:47274018..47276189-chr11:47289692..47292205,2	MCF-7	breast:
2	chr11:47273288..47275375-chr11:47288346..47292837,4	K562	blood:
3	chr11:47236362..47238989-chr11:47273774..47276751,3	K562	blood:
4	chr11:47207035..47209076-chr11:47274353..47276041,2	K562	blood:
5	chr11:47274831..47277970-chr11:47278025..47280120,3	K562	blood:
6	chr11:47273867..47276931-chr11:47289002..47291937,3	MCF-7	breast:
7	chr11:47265054..47272453-chr11:47272862..47282933,17	MCF-7	breast:
8	chr11:47236362..47238989-chr11:47273774..47276076,2	K562	blood:
9	chr11:47269243..47272486-chr11:47273981..47276768,5	MCF-7	breast:
10	chr11:47273086..47275375-chr11:47290934..47292611,2	K562	blood:
11	chr11:47268932..47273259-chr11:47273972..47277777,9	K562	blood:

No data

Variant related genes	Relation type
ACP2	TF binding region
NR1H3	TF binding region
ENSG00000025434	Chromatin interaction
ENSG00000134575	Chromatin interaction
ENSG00000134574	Chromatin interaction
ENSG00000110514	Chromatin interaction
ENSG00000165912	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10501321	0.86[MEX][hapmap];0.81[TSI][hapmap]
rs1051006	0.86[MEX][hapmap]
rs1052373	0.81[ASW][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.83[YRI][hapmap]
rs1055510	0.81[AMR][1000 genomes]
rs10769253	0.86[MEX][hapmap]
rs10769255	0.86[MEX][hapmap]
rs10838687	0.81[MEX][hapmap]
rs10838689	0.86[MEX][hapmap]
rs10838692	0.81[ASW][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.83[YRI][hapmap]
rs11039119	0.83[CHD][hapmap]
rs11039166	0.86[YRI][hapmap]
rs11600668	0.83[CHD][hapmap]
rs1375688	0.83[YRI][hapmap]
rs1449627	0.81[ASW][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.86[YRI][hapmap];0.81[AMR][1000 genomes]
rs16938581	0.88[AFR][1000 genomes]
rs2013867	0.84[CEU][hapmap];0.82[CHB][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.91[AMR][1000 genomes]
rs2029298	0.86[CHD][hapmap]
rs2167079	0.84[CEU][hapmap];0.82[CHB][hapmap];0.91[MEX][hapmap];0.88[AMR][1000 genomes]
rs2242261	0.88[LWK][hapmap];0.85[MEX][hapmap];0.92[MKK][hapmap];0.83[YRI][hapmap];0.88[AFR][1000 genomes]
rs2242262	0.83[YRI][hapmap];0.88[AFR][1000 genomes]
rs2279238	0.82[CHB][hapmap];0.86[MEX][hapmap]
rs2279239	0.82[AMR][1000 genomes]
rs2290146	0.81[MEX][hapmap]
rs2290148	0.81[MEX][hapmap]
rs2306353	0.84[AFR][1000 genomes]
rs326214	0.86[MEX][hapmap]
rs326222	0.84[CEU][hapmap];0.82[CHB][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes]
rs35879051	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3758669	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs3758670	0.85[AFR][1000 genomes]
rs3758673	0.87[ASW][hapmap];0.86[CHB][hapmap];0.89[LWK][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.90[YRI][hapmap];0.82[AMR][1000 genomes]
rs3781619	0.80[CHD][hapmap];0.86[MEX][hapmap];0.87[MKK][hapmap];0.80[YRI][hapmap]
rs3781620	0.86[AFR][1000 genomes]
rs3816725	0.81[ASW][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap]
rs4567413	0.86[CHD][hapmap]
rs4647741	0.81[AFR][1000 genomes]
rs4752972	0.88[AFR][1000 genomes]
rs4752973	0.86[MEX][hapmap]
rs4752977	0.81[MEX][hapmap]
rs4752983	0.86[MEX][hapmap]
rs59663860	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7109203	0.86[AMR][1000 genomes]
rs7118396	0.86[MEX][hapmap]
rs7120118	0.81[ASW][hapmap];0.84[CEU][hapmap];0.86[CHB][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.90[YRI][hapmap]
rs7120158	0.83[YRI][hapmap];0.88[AFR][1000 genomes]
rs7129661	0.90[AMR][1000 genomes]
rs7395496	0.80[YRI][hapmap]
rs7395581	0.87[ASW][hapmap];0.83[LWK][hapmap];0.80[TSI][hapmap];0.93[YRI][hapmap];0.89[AMR][1000 genomes]
rs753992	0.86[MEX][hapmap]
rs7933246	0.88[AFR][1000 genomes]
rs7937101	0.86[CHD][hapmap]
rs830083	0.81[AFR][1000 genomes]
rs830084	0.88[YRI][hapmap]
rs830085	0.87[ASW][hapmap];0.84[CEU][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.93[YRI][hapmap];0.93[AMR][1000 genomes]
rs901746	0.84[CEU][hapmap];0.82[CHB][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.89[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897323	chr11:47182926-47460306	Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv917316	chr11:47232210-47448882	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Metabolic syndrome	22399527	GWAS catalog

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs10838681	FNBP4	cis	cerebellum	SCAN
rs10838681	MADD	cis	cerebellum	SCAN
rs10838681	ENSG00000134575	cis	multi-tissue	Pritchard
rs10838681	ACP2	cis	multi-tissue	Pritchard
rs10838681	ACP2	cis	lymphoblastoid	seeQTL
rs10838681	MADD	cis	parietal	SCAN
rs10838681	DGKZ	cis	cerebellum	SCAN
rs10838681	NR1H3	cis	multi-tissue	Pritchard
rs10838681	DDB2	cis	lymphoblastoid	seeQTL
rs10838681	DDB2	cis	Lymphoblastoid	GTEx
rs10838681	NR1H3	cis	lymphoblastoid	seeQTL
rs10838681	NR1H3	cis	parietal	SCAN

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47271000-47280800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:47271200-47276200	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr11:47271200-47276600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr11:47271400-47275200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr11:47271400-47275200	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr11:47271400-47275200	Weak transcription	Brain Angular Gyrus	brain
7	chr11:47271400-47275200	Weak transcription	Brain Hippocampus Middle	brain
8	chr11:47271400-47275200	Weak transcription	Fetal Lung	lung
9	chr11:47271400-47275200	Weak transcription	Fetal Muscle Leg	muscle
10	chr11:47271400-47275200	Weak transcription	Fetal Thymus	thymus
11	chr11:47271400-47275200	Weak transcription	Psoas Muscle	Psoas
12	chr11:47271400-47275200	Weak transcription	Right Atrium	heart
13	chr11:47271400-47275200	Weak transcription	Right Ventricle	heart
14	chr11:47271400-47275200	Weak transcription	A549	lung
15	chr11:47271400-47275200	Weak transcription	HUVEC	blood vessel
16	chr11:47271400-47275200	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr11:47271400-47275400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr11:47271400-47275400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr11:47271400-47275400	Weak transcription	Primary hematopoietic stem cells	blood
20	chr11:47271400-47275400	Weak transcription	Brain Anterior Caudate	brain
21	chr11:47271400-47275400	Weak transcription	Brain Cingulate Gyrus	brain
22	chr11:47271400-47275400	Weak transcription	Brain Substantia Nigra	brain
23	chr11:47271400-47275400	Weak transcription	Fetal Heart	heart
24	chr11:47271400-47275400	Weak transcription	Fetal Kidney	kidney
25	chr11:47271400-47275400	Weak transcription	Fetal Muscle Trunk	muscle
26	chr11:47271400-47275400	Weak transcription	NHLF	lung
27	chr11:47271400-47275600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr11:47271400-47275600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr11:47271400-47275600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr11:47271400-47275600	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr11:47271400-47275600	Weak transcription	HSMM	muscle
32	chr11:47271400-47275600	Weak transcription	NH-A	brain
33	chr11:47271400-47275600	Weak transcription	NHDF-Ad	bronchial
34	chr11:47271400-47275600	Weak transcription	Osteobl	bone
35	chr11:47271400-47275800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr11:47271400-47275800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr11:47271400-47275800	Weak transcription	Primary B cells from cord blood	blood
38	chr11:47271400-47275800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr11:47271400-47275800	Weak transcription	Ovary	ovary
40	chr11:47271400-47276200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr11:47271400-47276400	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr11:47271400-47276400	Weak transcription	Gastric	stomach
43	chr11:47271400-47276600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr11:47271400-47276600	Weak transcription	Rectal Smooth Muscle	rectum
45	chr11:47271400-47278600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr11:47271400-47278600	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr11:47271400-47278600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr11:47271400-47278600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr11:47271400-47278600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr11:47271400-47278800	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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