Variant report

Variant	rs10838686
Chromosome Location	chr11:47311367-47311368
allele	G/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	chr11:47311101-47311533	GM12878	blood:	n/a	n/a
2	FOXP2	chr11:47311336-47311716	PFSK-1	brain:	n/a	n/a
3	POLR2A	chr11:47311095-47311887	K562	blood:	n/a	n/a
4	POLR2A	chr11:47311279-47311868	K562	blood:	n/a	n/a
5	CTCF	chr11:47311240-47311390	K562	blood:	n/a	chr11:47311327-47311336
6	POLR2A	chr11:47311142-47311928	K562	blood:	n/a	n/a
7	POLR2A	chr11:47311321-47311435	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr11:47311201-47311863	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:47304441..47308044-chr11:47308393..47311628,5	K562	blood:
2	chr11:47289567..47294786-chr11:47310778..47315538,7	MCF-7	breast:
3	chr11:47300470..47302272-chr11:47310622..47312521,2	MCF-7	breast:

Variant related genes	Relation type
MADD	TF binding region
ENSG00000256746	Chromatin interaction
ENSG00000110514	Chromatin interaction
ENSG00000025434	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1051006	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10769253	1.00[CEU][hapmap];0.87[CHB][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10769254	0.86[CHB][hapmap];0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs10769255	0.90[CEU][hapmap];0.91[CHB][hapmap];0.94[EUR][1000 genomes]
rs10838685	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10838687	0.87[CHB][hapmap];0.95[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10838689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11039148	0.81[EUR][1000 genomes]
rs11039155	0.89[EUR][1000 genomes]
rs11039189	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11493249	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11530166	0.95[AMR][1000 genomes]
rs11821917	0.81[CEU][hapmap]
rs11824864	0.81[CEU][hapmap]
rs12222581	0.83[AMR][1000 genomes]
rs12574081	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12574410	0.80[CEU][hapmap]
rs1449626	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17790804	0.81[CEU][hapmap]
rs2242262	0.80[CEU][hapmap]
rs2242511	0.89[CEU][hapmap]
rs2254240	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2279238	0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2290146	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2290148	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]
rs2305280	0.82[CHB][hapmap]
rs2306353	0.80[CEU][hapmap]
rs3729802	1.00[CEU][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3729804	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3729805	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3758670	0.81[EUR][1000 genomes]
rs3824866	0.80[CEU][hapmap];0.83[YRI][hapmap]
rs4752977	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4752978	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4752979	0.91[AMR][1000 genomes]
rs4752983	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58023804	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59567949	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6485751	0.91[AMR][1000 genomes]
rs7118396	0.82[YRI][hapmap];0.81[EUR][1000 genomes]
rs7124958	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7395496	0.80[CEU][hapmap]
rs753812	0.90[CEU][hapmap]
rs753992	1.00[CEU][hapmap];0.91[CHB][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs753993	0.87[CHB][hapmap];0.85[AMR][1000 genomes]
rs7928073	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10838686	DDB2	Cis_1M	lymphoblastoid	RTeQTL
rs10838686	ACP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 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	chr11:47295000-47323600	Strong transcription	Dnd41	blood
3	chr11:47295200-47319800	Strong transcription	Fetal Muscle Trunk	muscle
4	chr11:47295200-47320200	Strong transcription	Fetal Stomach	stomach
5	chr11:47295200-47321600	Strong transcription	Rectal Mucosa Donor 29	rectum
6	chr11:47295200-47323800	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr11:47295200-47326800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr11:47295400-47318200	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr11:47295400-47318800	Strong transcription	Thymus	Thymus
10	chr11:47295400-47319200	Strong transcription	Brain Cingulate Gyrus	brain
11	chr11:47295400-47319600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr11:47295400-47319600	Strong transcription	Fetal Brain Female	brain
13	chr11:47295400-47320800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr11:47295400-47321400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr11:47295400-47323800	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr11:47295400-47324800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr11:47295400-47324800	Strong transcription	Fetal Thymus	thymus
18	chr11:47295400-47340200	Strong transcription	Primary T helper cells PMA-I stimulated	--
19	chr11:47295400-47341000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr11:47295400-47352600	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr11:47295600-47319600	Strong transcription	Fetal Muscle Leg	muscle
22	chr11:47295600-47320000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr11:47295600-47320200	Strong transcription	Fetal Intestine Large	intestine
24	chr11:47295600-47321200	Strong transcription	Brain Germinal Matrix	brain
25	chr11:47295600-47321800	Strong transcription	Primary B cells from peripheral blood	blood
26	chr11:47295600-47323800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr11:47295600-47323800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr11:47295600-47324000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr11:47295600-47324200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr11:47295600-47324200	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr11:47295600-47338800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr11:47295800-47315800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr11:47295800-47319600	Strong transcription	Fetal Intestine Small	intestine
34	chr11:47295800-47319800	Strong transcription	Duodenum Smooth Muscle	Duodenum
35	chr11:47295800-47320000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr11:47295800-47322000	Strong transcription	Sigmoid Colon	Sigmoid Colon
37	chr11:47295800-47322400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr11:47295800-47340600	Strong transcription	Primary neutrophils fromperipheralblood	blood
39	chr11:47295800-47352800	Strong transcription	Duodenum Mucosa	Duodenum
40	chr11:47296000-47317200	Strong transcription	Pancreas	Pancrea
41	chr11:47296000-47317600	Strong transcription	Gastric	stomach
42	chr11:47296000-47318800	Strong transcription	H1 Cell Line	embryonic stem cell
43	chr11:47296000-47318800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr11:47296000-47319400	Strong transcription	Lung	lung
45	chr11:47296000-47319800	Strong transcription	Brain Anterior Caudate	brain
46	chr11:47296000-47320200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr11:47296000-47320400	Strong transcription	Brain Inferior Temporal Lobe	brain
48	chr11:47296000-47321400	Strong transcription	HUES6 Cell Line	embryonic stem cell
49	chr11:47296000-47321800	Strong transcription	Colonic Mucosa	Colon
50	chr11:47296000-47321800	Strong transcription	Ovary	ovary

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