Variant report

Variant	rs2290148
Chromosome Location	chr11:47346145-47346146
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:47346035-47346415	GM12878	blood:	n/a	n/a
2	POLR2A	chr11:47345656-47346559	K562	blood:	n/a	n/a
3	POLR2A	chr11:47345728-47346192	K562	blood:	n/a	n/a
4	POLR2A	chr11:47345760-47346664	K562	blood:	n/a	n/a
5	POLR2A	chr11:47345608-47346674	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:47345193..47348335-chr11:47348410..47351414,3	K562	blood:
2	chr11:47291167..47293193-chr11:47345602..47348128,2	K562	blood:

Variant related genes	Relation type
MADD	TF binding region
ENSG00000110514	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1051006	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1052373	0.86[MEX][hapmap]
rs10769253	1.00[CEU][hapmap];0.87[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10769254	0.86[CHB][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10769255	0.91[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10838663	0.80[CEU][hapmap]
rs10838681	0.81[MEX][hapmap]
rs10838685	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10838686	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10838687	0.94[ASW][hapmap];0.87[CHB][hapmap];0.81[CHD][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs10838689	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10838692	0.86[MEX][hapmap]
rs11039155	0.87[EUR][1000 genomes]
rs11039189	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11493249	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11530166	0.91[AMR][1000 genomes]
rs11821917	0.81[CEU][hapmap]
rs11824864	0.81[CEU][hapmap]
rs11828339	0.81[CEU][hapmap]
rs12222581	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs12574081	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12574410	0.80[CEU][hapmap]
rs1375688	0.81[AFR][1000 genomes]
rs1449626	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1449627	0.86[MEX][hapmap]
rs17198158	0.81[CEU][hapmap]
rs17790804	0.81[CEU][hapmap]
rs2242261	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]
rs2242262	0.80[CEU][hapmap];0.89[YRI][hapmap]
rs2242511	0.89[CEU][hapmap]
rs2254240	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2279238	0.94[ASW][hapmap];0.80[CEU][hapmap];0.81[CHD][hapmap];0.90[GIH][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2290146	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2305280	0.94[ASW][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];0.83[LWK][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes]
rs2306353	0.80[CEU][hapmap]
rs2957873	0.87[ASW][hapmap];0.82[YRI][hapmap]
rs3729802	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3729804	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3729805	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3781619	0.94[ASW][hapmap];0.80[CEU][hapmap];0.90[GIH][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.83[TSI][hapmap];0.86[YRI][hapmap]
rs3816725	0.82[MEX][hapmap]
rs3824866	0.80[CEU][hapmap]
rs3847502	0.81[AFR][1000 genomes]
rs3847503	0.81[CEU][hapmap]
rs4752824	0.81[AFR][1000 genomes]
rs4752825	0.81[AFR][1000 genomes]
rs4752839	0.81[CEU][hapmap]
rs4752965	0.80[CEU][hapmap]
rs4752973	0.87[ASW][hapmap];0.95[MEX][hapmap];0.82[YRI][hapmap]
rs4752977	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4752978	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4752979	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes]
rs4752983	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58023804	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59567949	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6485751	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes]
rs7118396	0.94[ASW][hapmap];0.80[CEU][hapmap];0.81[CHD][hapmap];0.90[GIH][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap]
rs7120158	0.89[YRI][hapmap]
rs7124958	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];0.99[ASN][1000 genomes]
rs7127907	0.81[AFR][1000 genomes]
rs7395496	0.80[CEU][hapmap];0.86[YRI][hapmap]
rs753812	0.90[CEU][hapmap]
rs753992	1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs753993	0.87[CHB][hapmap];0.91[AMR][1000 genomes]
rs7928073	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7940809	0.81[AFR][1000 genomes]
rs830084	0.92[YRI][hapmap]
rs9666924	0.81[CEU][hapmap]

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	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
3	esv3330173	chr11:47289256-47450681	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
4	esv3416377	chr11:47289276-47450651	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
5	nsv832141	chr11:47333180-47520993	Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2290148	PTPMT1	cis	parietal	SCAN
rs2290148	DDB2	Cis_1M	lymphoblastoid	RTeQTL
rs2290148	ACP2	cis	Thyroid	GTEx
rs2290148	MADD	cis	lymphoblastoid	seeQTL
rs2290148	ACP2	Cis_1M	lymphoblastoid	RTeQTL
rs2290148	DDB2	cis	lymphoblastoid	seeQTL
rs2290148	ACP2	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47294600-47355200	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr11:47295400-47352600	Strong transcription	Primary T helper cells fromperipheralblood	blood
3	chr11:47295800-47352800	Strong transcription	Duodenum Mucosa	Duodenum
4	chr11:47296000-47353600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr11:47311800-47348800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr11:47323400-47352400	Strong transcription	Thymus	Thymus
7	chr11:47324200-47354600	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr11:47324600-47346800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr11:47324800-47352600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr11:47325000-47352400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr11:47325000-47352800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr11:47325200-47347000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr11:47325400-47346600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr11:47325400-47349200	Strong transcription	Fetal Thymus	thymus
15	chr11:47325400-47353000	Strong transcription	Fetal Intestine Small	intestine
16	chr11:47326000-47353600	Strong transcription	Fetal Stomach	stomach
17	chr11:47327800-47352200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr11:47328200-47351400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr11:47333000-47349400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr11:47333400-47346200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr11:47333800-47350600	Weak transcription	Psoas Muscle	Psoas
22	chr11:47336400-47350400	Weak transcription	HMEC	breast
23	chr11:47336600-47346800	Weak transcription	NHDF-Ad	bronchial
24	chr11:47337400-47348400	Weak transcription	Small Intestine	intestine
25	chr11:47338800-47347200	Weak transcription	Fetal Heart	heart
26	chr11:47338800-47356200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr11:47339000-47346800	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr11:47339200-47353000	Weak transcription	NH-A	brain
29	chr11:47340200-47352800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr11:47340400-47348600	Weak transcription	Osteobl	bone
31	chr11:47342000-47351800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr11:47342200-47346200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr11:47342200-47347000	Strong transcription	Skeletal Muscle Male	skeletal muscle
34	chr11:47342200-47348600	Strong transcription	Muscle Satellite Cultured Cells	--
35	chr11:47342200-47350200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr11:47342200-47352400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr11:47342200-47353200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr11:47342400-47349600	Strong transcription	Primary B cells from peripheral blood	blood
39	chr11:47342400-47350400	Strong transcription	Fetal Muscle Leg	muscle
40	chr11:47342400-47352000	Strong transcription	Rectal Mucosa Donor 29	rectum
41	chr11:47342400-47352400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr11:47342400-47352600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr11:47342600-47349800	Strong transcription	Fetal Muscle Trunk	muscle
44	chr11:47342600-47350400	Strong transcription	Adipose Nuclei	Adipose
45	chr11:47342600-47350600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr11:47342600-47350800	Strong transcription	Stomach Smooth Muscle	stomach
47	chr11:47342600-47350800	Strong transcription	HepG2	liver
48	chr11:47342600-47351200	Strong transcription	Fetal Lung	lung
49	chr11:47342600-47351600	Strong transcription	Hela-S3	cervix
50	chr11:47342600-47351800	Strong transcription	Rectal Mucosa Donor 31	rectum

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