Variant report

Variant	rs7944584
Chromosome Location	chr11:47336320-47336321
allele	A/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:

Extended variants
information (count: 26 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10501320	0.91[CEU][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10838696	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MKK][hapmap];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11039114	1.00[ASW][hapmap]
rs11039130	0.82[CHB][hapmap];0.82[ASN][1000 genomes]
rs11039138	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs11039139	0.94[ASN][1000 genomes]
rs11039149	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11039154	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11039159	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11039162	0.83[ASN][1000 genomes]
rs11039165	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11039182	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11039183	1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11606683	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MKK][hapmap];0.83[ASN][1000 genomes]
rs11988	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2167080	0.94[ASN][1000 genomes]
rs2596407	0.94[ASN][1000 genomes]
rs2697923	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2856653	0.94[ASN][1000 genomes]
rs749067	0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[MKK][hapmap];0.83[ASN][1000 genomes]
rs7944419	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][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

Variant related diseases (count:2)

Disease	PMID	Source
Fasting glucose-related traits (interaction with BMI)	22581228	GWAS catalog
Fasting glucose-related traits	20081858	GWAS catalog

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7944584	MTCH2	cis	cerebellum	SCAN
rs7944584	FNBP4	Cis_1M	lymphoblastoid	RTeQTL
rs7944584	TP53I11	cis	parietal	SCAN
rs7944584	MADD	cis	parietal	SCAN

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	chr11:47325200-47337000	Strong transcription	Duodenum Smooth Muscle	Duodenum
26	chr11:47325200-47340400	Strong transcription	Sigmoid Colon	Sigmoid Colon
27	chr11:47325200-47341000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr11:47325200-47344000	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr11:47325200-47347000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr11:47325400-47341400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr11:47325400-47346600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr11:47325400-47349200	Strong transcription	Fetal Thymus	thymus
33	chr11:47325400-47353000	Strong transcription	Fetal Intestine Small	intestine
34	chr11:47326000-47353600	Strong transcription	Fetal Stomach	stomach
35	chr11:47326200-47337000	Strong transcription	Rectal Mucosa Donor 31	rectum
36	chr11:47327400-47341200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr11:47327600-47340400	Strong transcription	Fetal Muscle Trunk	muscle
38	chr11:47327800-47352200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr11:47328000-47340600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr11:47328000-47341000	Strong transcription	Adipose Nuclei	Adipose
41	chr11:47328200-47351400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr11:47328400-47340400	Strong transcription	Skeletal Muscle Male	skeletal muscle
43	chr11:47329000-47341000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr11:47329200-47337000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr11:47329200-47340400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr11:47329400-47339600	Strong transcription	Left Ventricle	heart
47	chr11:47329600-47339200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr11:47329600-47340400	Strong transcription	Brain Hippocampus Middle	brain
49	chr11:47329800-47339000	Strong transcription	Muscle Satellite Cultured Cells	--
50	chr11:47329800-47339200	Strong transcription	Cortex derived primary cultured neurospheres	brain

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