Variant report

Variant	rs2658801
Chromosome Location	chr11:93216751-93216752
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	chr11:93215734..93218245-chr11:93228402..93230678,2	MCF-7	breast:

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10734161	0.84[ASN][1000 genomes]
rs2124558	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.92[TSI][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2605597	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2605612	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2608272	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2608279	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2608280	0.84[ASN][1000 genomes]
rs2658798	0.81[ASW][hapmap];1.00[CEU][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7106781	0.83[ASN][1000 genomes]
rs897906	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][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	nsv1039134	chr11:92790000-93219942	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv898181	chr11:93072843-93662459	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
3	nsv1039623	chr11:93141461-93328739	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	esv2760208	chr11:93172673-93266594	Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2658801	MTNR1B	cis	parietal	SCAN

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:93207000-93239000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr11:93207800-93220000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr11:93208200-93223200	Weak transcription	GM12878-XiMat	blood
4	chr11:93208400-93218400	Weak transcription	Left Ventricle	heart
5	chr11:93208600-93217800	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr11:93209000-93231400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr11:93209000-93235200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr11:93209200-93229200	Weak transcription	Dnd41	blood
9	chr11:93209400-93218800	Strong transcription	Fetal Intestine Small	intestine
10	chr11:93209600-93229400	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr11:93209800-93217200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr11:93210600-93220000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr11:93210600-93231600	Weak transcription	A549	lung
14	chr11:93211000-93218600	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr11:93211000-93225800	Weak transcription	Thymus	Thymus
16	chr11:93211000-93253400	Weak transcription	Primary T cells from cord blood	blood
17	chr11:93211200-93222000	Weak transcription	Adipose Nuclei	Adipose
18	chr11:93211600-93219000	Weak transcription	HepG2	liver
19	chr11:93211600-93220400	Weak transcription	Brain Cingulate Gyrus	brain
20	chr11:93211600-93223000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr11:93211600-93243800	Weak transcription	Fetal Thymus	thymus
22	chr11:93211800-93218600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr11:93211800-93220200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr11:93212000-93220000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr11:93212200-93218000	Weak transcription	Ovary	ovary
26	chr11:93212200-93220600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr11:93212200-93221200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr11:93212200-93222800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr11:93212200-93234800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr11:93212400-93222600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr11:93212400-93225800	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr11:93212800-93217000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr11:93213000-93217200	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr11:93213000-93219200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr11:93213000-93220400	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr11:93213000-93221200	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr11:93213000-93221400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr11:93213400-93218800	Enhancers	Fetal Brain Male	brain
39	chr11:93213600-93217000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr11:93214400-93218200	Enhancers	Cortex derived primary cultured neurospheres	brain
41	chr11:93214400-93221200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr11:93214600-93217400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr11:93214800-93220200	Weak transcription	Aorta	Aorta
44	chr11:93214800-93234400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr11:93215000-93217400	Strong transcription	Fetal Intestine Large	intestine
46	chr11:93215000-93217600	Weak transcription	Hela-S3	cervix
47	chr11:93215200-93217400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr11:93215200-93218000	Weak transcription	Pancreas	Pancrea
49	chr11:93215200-93218400	Weak transcription	Esophagus	oesophagus
50	chr11:93215200-93220800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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