Variant report

Variant	rs10838687
Chromosome Location	chr11:47312892-47312893
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	chr11:47312650-47313173	K562	blood:	n/a	n/a
2	POLR2A	chr11:47312707-47313576	K562	blood:	n/a	n/a
3	FOXA1	chr11:47312822-47313065	T-47D	breast:	n/a	n/a
4	STAT1	chr11:47312482-47312968	Hela-S3	cervix:	n/a	chr11:47312687-47312707 chr11:47312692-47312701 chr11:47312690-47312704 chr11:47312693-47312702

No.	Distal block	Cell Line	Cell type
1	chr11:47295273..47297466-chr11:47311711..47313688,2	MCF-7	breast:
2	chr11:47301179..47303619-chr11:47311417..47313779,2	K562	blood:
3	chr11:47289567..47294786-chr11:47310778..47315538,7	MCF-7	breast:

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

Extended variants
information (count: 65 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10501321	0.83[CHB][hapmap]
rs1051006	0.82[ASW][hapmap];0.87[CHB][hapmap];0.81[CHD][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.92[AMR][1000 genomes]
rs1052373	0.82[ASW][hapmap];0.83[CHB][hapmap];0.89[LWK][hapmap];0.86[MEX][hapmap];0.94[MKK][hapmap]
rs1055510	0.87[AFR][1000 genomes]
rs10742799	0.83[AFR][1000 genomes]
rs10769253	0.95[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes]
rs10769255	0.95[MEX][hapmap];0.81[TSI][hapmap]
rs10838681	0.81[MEX][hapmap]
rs10838685	0.88[AMR][1000 genomes]
rs10838686	0.87[CHB][hapmap];0.95[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10838689	0.87[CHB][hapmap];0.95[MEX][hapmap];0.89[AMR][1000 genomes]
rs10838692	0.82[ASW][hapmap];0.83[CHB][hapmap];0.80[CHD][hapmap];0.87[LWK][hapmap];0.86[MEX][hapmap];0.94[MKK][hapmap];0.84[AFR][1000 genomes]
rs11039166	0.83[CHB][hapmap];0.83[YRI][hapmap]
rs11530166	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12222581	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12575456	0.82[AFR][1000 genomes]
rs1375688	0.83[CHB][hapmap];0.84[AFR][1000 genomes]
rs1449626	0.92[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1449627	0.82[ASW][hapmap];0.83[CHB][hapmap];0.80[CHD][hapmap];0.89[LWK][hapmap];0.86[MEX][hapmap];0.94[MKK][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes]
rs2242261	0.88[ASW][hapmap];0.95[MEX][hapmap];0.86[YRI][hapmap]
rs2242262	0.86[YRI][hapmap]
rs2254240	0.88[AMR][1000 genomes]
rs2279238	0.88[ASW][hapmap];0.95[MEX][hapmap];0.92[AMR][1000 genomes]
rs2290146	0.94[ASW][hapmap];0.87[CHB][hapmap];0.81[CHD][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs2290148	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]
rs2305280	1.00[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.81[MKK][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2596397	0.81[EUR][1000 genomes]
rs2957873	0.94[ASW][hapmap];0.84[CEU][hapmap];0.80[CHD][hapmap];0.92[GIH][hapmap];0.82[LWK][hapmap];0.85[TSI][hapmap];0.93[YRI][hapmap];0.81[EUR][1000 genomes]
rs326214	0.82[CHB][hapmap];0.80[CHD][hapmap]
rs3729802	0.86[AMR][1000 genomes]
rs3729804	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs3729805	0.88[AMR][1000 genomes]
rs3758673	0.83[MKK][hapmap]
rs3781619	0.88[ASW][hapmap];0.95[MEX][hapmap];0.83[YRI][hapmap]
rs3781621	0.86[AFR][1000 genomes]
rs3781622	0.83[CHB][hapmap];0.80[AFR][1000 genomes]
rs3816725	0.82[ASW][hapmap];0.83[CHB][hapmap];0.82[MEX][hapmap];0.90[MKK][hapmap]
rs3847502	0.84[AFR][1000 genomes]
rs4647757	0.81[EUR][1000 genomes]
rs4752824	0.84[AFR][1000 genomes]
rs4752825	0.84[AFR][1000 genomes]
rs4752973	0.94[ASW][hapmap];0.84[CEU][hapmap];0.82[CHD][hapmap];0.92[GIH][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.85[TSI][hapmap];0.93[YRI][hapmap];0.83[EUR][1000 genomes]
rs4752977	0.94[ASW][hapmap];0.87[CHB][hapmap];0.81[CHD][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4752978	0.93[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4752979	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4752983	0.88[ASW][hapmap];0.87[CHB][hapmap];0.81[CHD][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.91[AMR][1000 genomes]
rs58023804	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs59567949	0.92[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs61896050	0.87[AFR][1000 genomes]
rs6485751	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7118396	0.88[ASW][hapmap];0.95[MEX][hapmap]
rs7120158	0.86[YRI][hapmap]
rs7124955	0.83[CHB][hapmap]
rs7124958	0.87[CHB][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs7127907	0.84[AFR][1000 genomes]
rs7395496	0.83[YRI][hapmap]
rs753992	0.95[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes]
rs753993	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7928073	0.82[AMR][1000 genomes]
rs7940809	0.84[AFR][1000 genomes]
rs830084	0.85[YRI][hapmap]

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

Variant related diseases (count:1)

Disease	PMID	Source
Proinsulin levels	21873549	GWAS catalog

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs10838687	ACP2	Cis_1M	lymphoblastoid	RTeQTL
rs10838687	MADD	cis	lymphoblastoid	seeQTL
rs10838687	ACP2	cis	multi-tissue	Pritchard
rs10838687	DDB2	cis	lymphoblastoid	seeQTL
rs10838687	ACP2	cis	Thyroid	GTEx
rs10838687	MTCH2	cis	cerebellum	SCAN
rs10838687	PTPMT1	cis	parietal	SCAN
rs10838687	ACP2	cis	lymphoblastoid	seeQTL

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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