Variant report

Variant	rs2242261
Chromosome Location	chr11:47266808-47266809
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:47266624-47266906	K562	blood:	n/a	n/a
2	POLR2A	chr11:47266192-47267723	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr11:47266685-47266946	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr11:47266259-47267318	A549	lung:	n/a	n/a
5	POLR2A	chr11:47266493-47266958	HepG2	liver:	n/a	n/a
6	POLR2A	chr11:47266138-47266850	SK-N-MC	brain:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:47236414..47239398-chr11:47265054..47267561,5	K562	blood:
2	chr11:47205996..47209414-chr11:47263017..47267262,4	MCF-7	breast:
3	chr11:47264797..47267629-chr11:47289343..47292246,3	K562	blood:
4	chr11:47263774..47268457-chr11:47268937..47272422,6	MCF-7	breast:
5	chr11:47263865..47272320-chr11:47288426..47294726,14	MCF-7	breast:
6	chr11:47265054..47272453-chr11:47272862..47282933,17	MCF-7	breast:
7	chr11:47236332..47238351-chr11:47265199..47266819,2	MCF-7	breast:

No data

Variant related genes	Relation type
ACP2	TF binding region
NR1H3	TF binding region
ENSG00000165912	Chromatin interaction
ENSG00000110514	Chromatin interaction
ENSG00000025434	Chromatin interaction
ENSG00000134574	Chromatin interaction
ENSG00000256746	Chromatin interaction
ENSG00000134575	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1051006	0.93[ASW][hapmap];0.80[CEU][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.80[AMR][1000 genomes]
rs1052373	0.81[MEX][hapmap]
rs10742797	0.81[JPT][hapmap]
rs10769253	0.80[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs10769255	0.87[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs10838663	1.00[CEU][hapmap]
rs10838681	0.88[LWK][hapmap];0.85[MEX][hapmap];0.92[MKK][hapmap];0.83[YRI][hapmap];0.88[AFR][1000 genomes]
rs10838685	0.81[EUR][1000 genomes]
rs10838687	0.88[ASW][hapmap];0.95[MEX][hapmap];0.86[YRI][hapmap]
rs10838689	0.81[ASW][hapmap];0.80[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs10838692	0.81[MEX][hapmap]
rs11039144	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11039148	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11039155	0.87[EUR][1000 genomes]
rs12574081	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12574410	1.00[CEU][hapmap]
rs1449626	0.80[AMR][1000 genomes]
rs1449627	0.81[MEX][hapmap]
rs16938581	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2242262	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2279238	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.89[YRI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2290146	0.94[ASW][hapmap];0.80[CEU][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.89[YRI][hapmap]
rs2290148	0.94[ASW][hapmap];0.80[CEU][hapmap];0.81[CHD][hapmap];0.90[GIH][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.83[TSI][hapmap];0.89[YRI][hapmap]
rs2305280	0.88[ASW][hapmap]
rs2306353	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2596397	0.89[AMR][1000 genomes]
rs2596398	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2633080	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2633083	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2957873	0.94[ASW][hapmap];0.82[CHB][hapmap];0.88[LWK][hapmap];0.81[MEX][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs326224	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3729802	0.85[CEU][hapmap];0.80[YRI][hapmap]
rs3758670	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3781619	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3781620	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3824866	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4647725	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4647726	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4647737	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4647741	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4647754	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4647757	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs4752965	1.00[CEU][hapmap]
rs4752972	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4752973	0.94[ASW][hapmap];0.86[CHB][hapmap];0.80[CHD][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4752977	0.94[ASW][hapmap];0.80[CEU][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.83[TSI][hapmap];0.93[YRI][hapmap];0.81[AMR][1000 genomes]
rs4752983	1.00[ASW][hapmap];0.80[CEU][hapmap];0.81[CHD][hapmap];0.90[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.86[YRI][hapmap]
rs59567949	0.80[AMR][1000 genomes]
rs7118396	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7120118	0.81[MEX][hapmap]
rs7120158	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7124958	0.88[YRI][hapmap]
rs7395496	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs753992	0.80[CEU][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs7933246	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7947269	0.83[AMR][1000 genomes]
rs830083	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs830084	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs830085	0.80[LWK][hapmap];0.81[MEX][hapmap]

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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2242261	NR1H3	cis	lymphoblastoid	seeQTL
rs2242261	ACP2	cis	lymphoblastoid	seeQTL
rs2242261	ACP2	cis	Thyroid	GTEx
rs2242261	PTPMT1	cis	parietal	SCAN
rs2242261	DDB2	cis	lymphoblastoid	seeQTL
rs2242261	ACP2	Cis_1M	lymphoblastoid	RTeQTL
rs2242261	MADD	cis	lymphoblastoid	seeQTL
rs2242261	DDB2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47238400-47269400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:47242400-47269200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr11:47243600-47269200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr11:47246600-47267800	Strong transcription	HUES6 Cell Line	embryonic stem cell
5	chr11:47247400-47267600	Strong transcription	Thymus	Thymus
6	chr11:47254600-47267800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr11:47255400-47269200	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr11:47255600-47268800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr11:47255800-47267600	Strong transcription	H1 Cell Line	embryonic stem cell
10	chr11:47256000-47268000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr11:47256200-47267800	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr11:47256400-47267800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr11:47256800-47268800	Strong transcription	Fetal Thymus	thymus
14	chr11:47257800-47267800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr11:47257800-47268000	Strong transcription	Cortex derived primary cultured neurospheres	brain
16	chr11:47258000-47269000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr11:47258200-47267600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr11:47258400-47267800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr11:47258400-47268400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr11:47258600-47267800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr11:47258600-47267800	Strong transcription	Rectal Smooth Muscle	rectum
22	chr11:47258600-47268800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr11:47258800-47267400	Strong transcription	Colon Smooth Muscle	Colon
24	chr11:47258800-47268000	Strong transcription	NHEK	skin
25	chr11:47259000-47268200	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr11:47259000-47268800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr11:47259000-47269000	Strong transcription	Fetal Stomach	stomach
28	chr11:47259200-47268000	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr11:47259400-47267400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr11:47259400-47267600	Strong transcription	Duodenum Mucosa	Duodenum
31	chr11:47259400-47267600	Strong transcription	Duodenum Smooth Muscle	Duodenum
32	chr11:47259400-47267600	Strong transcription	Fetal Lung	lung
33	chr11:47259400-47267600	Strong transcription	Rectal Mucosa Donor 31	rectum
34	chr11:47259400-47267800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
35	chr11:47259400-47267800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr11:47259400-47267800	Strong transcription	Primary T cells from cord blood	blood
37	chr11:47259400-47267800	Strong transcription	Primary hematopoietic stem cells	blood
38	chr11:47259400-47267800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr11:47259400-47267800	Strong transcription	Gastric	stomach
40	chr11:47259400-47268000	Strong transcription	Brain Anterior Caudate	brain
41	chr11:47259400-47268000	Strong transcription	Stomach Smooth Muscle	stomach
42	chr11:47259400-47268800	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr11:47259400-47268800	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr11:47259400-47269000	Strong transcription	Primary B cells from peripheral blood	blood
45	chr11:47259400-47269000	Strong transcription	Sigmoid Colon	Sigmoid Colon
46	chr11:47259600-47267000	Strong transcription	Brain Germinal Matrix	brain
47	chr11:47259600-47267400	Strong transcription	Aorta	Aorta
48	chr11:47259600-47267800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr11:47259600-47267800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr11:47259600-47268600	Strong transcription	Brain Inferior Temporal Lobe	brain

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