Variant report

Variant	rs4756042
Chromosome Location	chr11:45957478-45957479
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	chr11:45957196..45959472-chr11:45964633..45967453,2	MCF-7	breast:
2	chr11:45944975..45945724-chr11:45956686..45957579,2	K562	blood:

Variant related genes	Relation type
ENSG00000135365	Chromatin interaction
ENSG00000165905	Chromatin interaction

Extended variants
information (count: 112 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs10128629	1.00[ASN][1000 genomes]
rs1038733	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs10734539	1.00[ASN][1000 genomes]
rs10734540	1.00[ASN][1000 genomes]
rs10742773	1.00[CEU][hapmap];0.89[GIH][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10769177	0.93[AFR][1000 genomes]
rs10838528	1.00[ASN][1000 genomes]
rs10838537	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs10838558	1.00[CEU][hapmap]
rs10838563	1.00[ASN][1000 genomes]
rs10838564	1.00[CEU][hapmap]
rs11820849	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs11820877	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11827687	1.00[CEU][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11827732	1.00[ASN][1000 genomes]
rs11828167	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1401420	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1401421	1.00[CEU][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1490082	1.00[ASN][1000 genomes]
rs1490087	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs1565412	1.00[CEU][hapmap]
rs16938429	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16938437	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];0.92[LWK][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1907003	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs1973721	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1994599	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs2013010	1.00[CEU][hapmap]
rs2130469	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs2130470	1.00[ASN][1000 genomes]
rs2130471	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs2130473	1.00[ASN][1000 genomes]
rs2171895	1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs2860376	0.89[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2860433	1.00[CEU][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2863714	1.00[CEU][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2932510	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs2932512	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs2932515	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs2932516	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs2945996	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2945998	1.00[CEU][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2946000	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2946002	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2946005	1.00[CEU][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2946008	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2946009	1.00[CEU][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2959082	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs2959083	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs2959085	1.00[CEU][hapmap]
rs2959088	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2959089	0.84[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2959095	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2959096	1.00[CEU][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2959097	1.00[CEU][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2959103	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2959104	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs3929339	1.00[CEU][hapmap]
rs4237661	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs4281461	1.00[ASN][1000 genomes]
rs4756043	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4756048	1.00[CEU][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4756056	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs4756057	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs4756058	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[ASN][1000 genomes]
rs4756059	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs55945697	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61652532	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61882507	1.00[ASN][1000 genomes]
rs61882508	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61882509	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61882510	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61882511	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61882513	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61882514	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61882534	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61882535	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61882536	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61882538	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61882539	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61882540	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61882541	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61882542	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61882543	1.00[ASN][1000 genomes]
rs61882544	1.00[ASN][1000 genomes]
rs61882545	1.00[ASN][1000 genomes]
rs61882546	1.00[ASN][1000 genomes]
rs61882547	1.00[ASN][1000 genomes]
rs6485660	1.00[CEU][hapmap]
rs6485663	1.00[CEU][hapmap]
rs6485664	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs7103299	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs7106689	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs7111900	1.00[ASN][1000 genomes]
rs7120227	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs7125387	1.00[ASN][1000 genomes]
rs7129942	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs7130282	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73452216	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7397035	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs7478883	1.00[ASN][1000 genomes]
rs7924996	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs7932895	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7934407	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs7934572	1.00[CEU][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7934681	1.00[CEU][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7937896	1.00[CEU][hapmap]
rs7942083	1.00[CEU][hapmap]
rs7942246	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs7946524	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs939106	1.00[CEU][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv897314	chr11:45816020-45965129	Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv516442	chr11:45899962-45983385	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4756042	NR1H3	cis	multi-tissue	Pritchard

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:45945200-45969400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr11:45950200-45960000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr11:45951600-45959600	Strong transcription	H1 Cell Line	embryonic stem cell
4	chr11:45951800-45960000	Strong transcription	Aorta	Aorta
5	chr11:45951800-45960200	Strong transcription	Cortex derived primary cultured neurospheres	brain
6	chr11:45952000-45967000	Weak transcription	Fetal Kidney	kidney
7	chr11:45952400-45958200	Weak transcription	Psoas Muscle	Psoas
8	chr11:45952400-45959800	Strong transcription	Fetal Intestine Small	intestine
9	chr11:45952400-45960200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr11:45952400-45960200	Strong transcription	Fetal Muscle Leg	muscle
11	chr11:45952400-45996200	Weak transcription	Stomach Mucosa	stomach
12	chr11:45952800-45957800	Strong transcription	Brain Hippocampus Middle	brain
13	chr11:45952800-45959800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr11:45952800-45960200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr11:45952800-45960200	Strong transcription	Duodenum Mucosa	Duodenum
16	chr11:45952800-45961200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr11:45953000-45959000	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr11:45953000-45960000	Strong transcription	Brain Anterior Caudate	brain
19	chr11:45953000-45960200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr11:45953000-45960200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr11:45953000-45988600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr11:45953200-45957800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr11:45953200-45958400	Strong transcription	Brain Cingulate Gyrus	brain
24	chr11:45953200-45958400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr11:45953200-45958800	Strong transcription	Lung	lung
26	chr11:45953200-45958800	Strong transcription	Rectal Smooth Muscle	rectum
27	chr11:45953200-45959800	Strong transcription	Brain Inferior Temporal Lobe	brain
28	chr11:45953200-45960000	Strong transcription	Duodenum Smooth Muscle	Duodenum
29	chr11:45953200-45960000	Strong transcription	Left Ventricle	heart
30	chr11:45953200-45960200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr11:45953200-45972600	Strong transcription	Fetal Intestine Large	intestine
32	chr11:45953200-45975400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr11:45953400-45957800	Strong transcription	Right Ventricle	heart
34	chr11:45953400-45958200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
35	chr11:45953400-45958800	Strong transcription	Rectal Mucosa Donor 31	rectum
36	chr11:45953400-45960000	Strong transcription	Dnd41	blood
37	chr11:45953400-45960200	Strong transcription	Primary T cells from cord blood	blood
38	chr11:45953400-45960200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr11:45953400-45960200	Strong transcription	Adipose Nuclei	Adipose
40	chr11:45953600-45959800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr11:45953600-45959800	Strong transcription	Sigmoid Colon	Sigmoid Colon
42	chr11:45953600-45959800	Strong transcription	Thymus	Thymus
43	chr11:45953600-45960000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr11:45953600-45961200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr11:45953800-45958000	Weak transcription	Fetal Heart	heart
46	chr11:45953800-45958600	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr11:45953800-45960000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr11:45953800-45960000	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr11:45953800-45960000	Strong transcription	Fetal Muscle Trunk	muscle
50	chr11:45953800-45960200	Strong transcription	Osteobl	bone

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