Variant report

Variant	rs11039183
Chromosome Location	chr11:47346940-47346941
allele	A/G
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	chr11:47346871-47347214	K562	blood:	n/a	n/a
2	POLR2A	chr11:47346750-47347692	K562	blood:	n/a	n/a
3	POLR2A	chr11:47346893-47346945	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: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10838662	0.90[LWK][hapmap]
rs10838696	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11039130	0.82[CHB][hapmap]
rs11039138	0.87[CEU][hapmap];1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs11039139	1.00[ASN][1000 genomes]
rs11039149	1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[ASN][1000 genomes]
rs11039159	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11039162	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11039165	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs11039182	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11606287	0.83[MEX][hapmap]
rs11606683	1.00[ASW][hapmap];0.88[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11988	0.84[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12802374	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2167080	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2596407	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2697923	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2856653	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7116451	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs749067	0.88[CEU][hapmap];0.82[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7944419	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7944584	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7950102	1.00[YRI][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11039183	MADD	cis	parietal	SCAN
rs11039183	OR4B1	cis	cerebellum	SCAN

Chromatin state (count:123 , 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	chr11:47324800-47352600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr11:47325000-47352400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr11:47325000-47352800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr11:47325200-47347000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr11:47325400-47349200	Strong transcription	Fetal Thymus	thymus
13	chr11:47325400-47353000	Strong transcription	Fetal Intestine Small	intestine
14	chr11:47326000-47353600	Strong transcription	Fetal Stomach	stomach
15	chr11:47327800-47352200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr11:47328200-47351400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr11:47333000-47349400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr11:47333800-47350600	Weak transcription	Psoas Muscle	Psoas
19	chr11:47336400-47350400	Weak transcription	HMEC	breast
20	chr11:47337400-47348400	Weak transcription	Small Intestine	intestine
21	chr11:47338800-47347200	Weak transcription	Fetal Heart	heart
22	chr11:47338800-47356200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr11:47339200-47353000	Weak transcription	NH-A	brain
24	chr11:47340200-47352800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr11:47340400-47348600	Weak transcription	Osteobl	bone
26	chr11:47342000-47351800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr11:47342200-47347000	Strong transcription	Skeletal Muscle Male	skeletal muscle
28	chr11:47342200-47348600	Strong transcription	Muscle Satellite Cultured Cells	--
29	chr11:47342200-47350200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr11:47342200-47352400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr11:47342200-47353200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr11:47342400-47349600	Strong transcription	Primary B cells from peripheral blood	blood
33	chr11:47342400-47350400	Strong transcription	Fetal Muscle Leg	muscle
34	chr11:47342400-47352000	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr11:47342400-47352400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr11:47342400-47352600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr11:47342600-47349800	Strong transcription	Fetal Muscle Trunk	muscle
38	chr11:47342600-47350400	Strong transcription	Adipose Nuclei	Adipose
39	chr11:47342600-47350600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr11:47342600-47350800	Strong transcription	Stomach Smooth Muscle	stomach
41	chr11:47342600-47350800	Strong transcription	HepG2	liver
42	chr11:47342600-47351200	Strong transcription	Fetal Lung	lung
43	chr11:47342600-47351600	Strong transcription	Hela-S3	cervix
44	chr11:47342600-47351800	Strong transcription	Rectal Mucosa Donor 31	rectum
45	chr11:47342600-47352200	Strong transcription	Primary T helper cells PMA-I stimulated	--
46	chr11:47342600-47352200	Strong transcription	Fetal Brain Female	brain
47	chr11:47342600-47352400	Strong transcription	Dnd41	blood
48	chr11:47342600-47352600	Strong transcription	Liver	Liver
49	chr11:47342600-47352600	Strong transcription	Brain Inferior Temporal Lobe	brain
50	chr11:47342600-47352600	Strong transcription	Placenta Amnion	Placenta Amnion

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