Variant report

Variant	rs2729372
Chromosome Location	chr11:57323893-57323894
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:57322219..57325038-chr11:57326684..57330533,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000156587	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs2234412	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2509896	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2649660	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2649661	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2729360	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2729361	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2729381	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2848623	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2848632	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2848633	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5847	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv530621	chr11:57139699-57703639	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	nsv1051032	chr11:57290124-57363064	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv541049	chr11:57290124-57363064	Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	nsv1052073	chr11:57297499-57362802	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	nsv541050	chr11:57297499-57362802	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	nsv832163	chr11:57299354-57481050	Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
9	nsv1040913	chr11:57315006-57696122	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2729372	SMTNL1	cis	Adipose Subcutaneous	GTEx
rs2729372	SMTNL1	cis	lung	GTEx
rs2729372	SMTNL1	cis	Thyroid	GTEx
rs2729372	TIMM10	Cis_1M	lymphoblastoid	RTeQTL
rs2729372	SMTNL1	cis	Artery Tibial	GTEx

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57299200-57333000	Weak transcription	Right Atrium	heart
2	chr11:57307200-57333600	Weak transcription	HMEC	breast
3	chr11:57309200-57333400	Weak transcription	Psoas Muscle	Psoas
4	chr11:57313000-57326800	Strong transcription	Thymus	Thymus
5	chr11:57313200-57327600	Strong transcription	Fetal Brain Female	brain
6	chr11:57313200-57330000	Strong transcription	Dnd41	blood
7	chr11:57313400-57327800	Strong transcription	Brain Germinal Matrix	brain
8	chr11:57313400-57328000	Strong transcription	Fetal Stomach	stomach
9	chr11:57313600-57327800	Strong transcription	Fetal Thymus	thymus
10	chr11:57313600-57328600	Strong transcription	Lung	lung
11	chr11:57314000-57326600	Strong transcription	Brain Anterior Caudate	brain
12	chr11:57314000-57328000	Strong transcription	Primary T helper cells PMA-I stimulated	--
13	chr11:57314000-57328200	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr11:57314000-57328600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr11:57314000-57330200	Strong transcription	Fetal Intestine Small	intestine
16	chr11:57314000-57330400	Strong transcription	Primary T cells from cord blood	blood
17	chr11:57314200-57326400	Strong transcription	Cortex derived primary cultured neurospheres	brain
18	chr11:57314200-57329800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr11:57314400-57326600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr11:57314600-57328000	Strong transcription	Sigmoid Colon	Sigmoid Colon
21	chr11:57314800-57327200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr11:57314800-57330600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr11:57315000-57328000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr11:57315000-57330000	Weak transcription	NHEK	skin
25	chr11:57315200-57328000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr11:57315200-57328000	Strong transcription	Fetal Intestine Large	intestine
27	chr11:57315200-57329600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr11:57315200-57329600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr11:57315200-57330600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr11:57315400-57329000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr11:57315600-57330600	Strong transcription	Fetal Muscle Leg	muscle
32	chr11:57315800-57327600	Strong transcription	Duodenum Smooth Muscle	Duodenum
33	chr11:57315800-57327800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr11:57315800-57327800	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr11:57315800-57328000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr11:57315800-57328200	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr11:57315800-57330000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr11:57315800-57330200	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr11:57315800-57330800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr11:57316000-57328000	Strong transcription	GM12878-XiMat	blood
41	chr11:57316200-57328000	Strong transcription	Primary neutrophils fromperipheralblood	blood
42	chr11:57316200-57328000	Strong transcription	Stomach Smooth Muscle	stomach
43	chr11:57316400-57329000	Strong transcription	Primary T killer memory cells from peripheral blood	blood
44	chr11:57316600-57327800	Strong transcription	Spleen	Spleen
45	chr11:57316800-57324800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr11:57316800-57326800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
47	chr11:57316800-57327000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr11:57316800-57328000	Strong transcription	Gastric	stomach
49	chr11:57316800-57329200	Strong transcription	Primary B cells from peripheral blood	blood
50	chr11:57316800-57329400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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