Variant report

Variant	rs7940809
Chromosome Location	chr11:47335341-47335342
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:47330644..47333199-chr11:47335190..47338022,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MYBPC3-1	chr11:47335106-47335371	expReg_chr11_3924_-

Extended variants
information (count: 64 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10501321	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1052373	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1055510	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10742799	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10742801	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10769252	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10838684	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10838687	0.84[AFR][1000 genomes]
rs10838690	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10838691	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10838692	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10838693	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11039156	0.86[EUR][1000 genomes]
rs11039166	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11039167	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12222581	0.85[AFR][1000 genomes]
rs12575456	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1375688	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1449627	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2013867	0.84[EUR][1000 genomes]
rs2167079	0.83[EUR][1000 genomes]
rs2269434	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2279239	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2290146	0.81[AFR][1000 genomes]
rs2290148	0.81[AFR][1000 genomes]
rs2301216	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2305280	0.86[AFR][1000 genomes]
rs326214	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs326217	0.81[ASN][1000 genomes]
rs326222	0.84[EUR][1000 genomes]
rs35879051	0.88[EUR][1000 genomes]
rs3758669	0.83[EUR][1000 genomes]
rs3758672	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3758673	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3781621	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3781622	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3816725	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3847502	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4752822	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4752824	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4752825	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4752979	0.88[AFR][1000 genomes]
rs4752980	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59663860	0.88[EUR][1000 genomes]
rs61896050	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6485746	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6485751	0.85[AFR][1000 genomes]
rs67871383	0.86[ASN][1000 genomes]
rs7109147	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7109203	0.80[EUR][1000 genomes]
rs7120118	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7120957	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7124955	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7124958	0.81[AFR][1000 genomes]
rs7127907	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7129661	0.85[EUR][1000 genomes]
rs7395581	0.82[EUR][1000 genomes]
rs830085	0.83[EUR][1000 genomes]
rs901746	0.84[EUR][1000 genomes]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7940809	ACP2	cis	Thyroid	GTEx
rs7940809	ACP2	Cis_1M	lymphoblastoid	RTeQTL
rs7940809	PACSIN3	cis	Esophagus Mucosa	GTEx

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	chr11:47295400-47340200	Strong transcription	Primary T helper cells PMA-I stimulated	--
3	chr11:47295400-47341000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr11:47295400-47352600	Strong transcription	Primary T helper cells fromperipheralblood	blood
5	chr11:47295600-47338800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr11:47295800-47340600	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr11:47295800-47352800	Strong transcription	Duodenum Mucosa	Duodenum
8	chr11:47296000-47353600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr11:47296200-47340400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr11:47300000-47341200	Strong transcription	Placenta	Placenta
11	chr11:47303200-47340600	Strong transcription	Hela-S3	cervix
12	chr11:47311800-47348800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr11:47322400-47341000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr11:47323400-47341600	Strong transcription	Rectal Mucosa Donor 29	rectum
15	chr11:47323400-47352400	Strong transcription	Thymus	Thymus
16	chr11:47324200-47354600	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr11:47324600-47341400	Strong transcription	Primary T cells from cord blood	blood
18	chr11:47324600-47346800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr11:47324800-47337200	Strong transcription	Dnd41	blood
20	chr11:47324800-47341000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr11:47324800-47352600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr11:47325000-47338600	Strong transcription	Primary B cells from peripheral blood	blood
23	chr11:47325000-47352400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr11:47325000-47352800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr11:47325200-47335600	Strong transcription	Brain Germinal Matrix	brain
26	chr11:47325200-47337000	Strong transcription	Duodenum Smooth Muscle	Duodenum
27	chr11:47325200-47340400	Strong transcription	Sigmoid Colon	Sigmoid Colon
28	chr11:47325200-47341000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr11:47325200-47344000	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr11:47325200-47347000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr11:47325400-47341400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr11:47325400-47346600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr11:47325400-47349200	Strong transcription	Fetal Thymus	thymus
34	chr11:47325400-47353000	Strong transcription	Fetal Intestine Small	intestine
35	chr11:47326000-47353600	Strong transcription	Fetal Stomach	stomach
36	chr11:47326200-47337000	Strong transcription	Rectal Mucosa Donor 31	rectum
37	chr11:47327400-47341200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr11:47327600-47340400	Strong transcription	Fetal Muscle Trunk	muscle
39	chr11:47327800-47336200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr11:47327800-47352200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr11:47328000-47340600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr11:47328000-47341000	Strong transcription	Adipose Nuclei	Adipose
43	chr11:47328200-47351400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr11:47328400-47340400	Strong transcription	Skeletal Muscle Male	skeletal muscle
45	chr11:47329000-47341000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr11:47329200-47337000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr11:47329200-47340400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr11:47329400-47339600	Strong transcription	Left Ventricle	heart
49	chr11:47329600-47335600	Strong transcription	Brain Anterior Caudate	brain
50	chr11:47329600-47339200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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