Variant report

Variant	rs1920397
Chromosome Location	chr3:150934318-150934319
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	chr3:150919820..150922068-chr3:150933502..150935019,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000174946	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1017348	1.00[CEU][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs10513387	0.89[CEU][hapmap]
rs1221002	1.00[CEU][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];0.92[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1221003	0.85[CEU][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1231519	0.85[CEU][hapmap];0.88[CHD][hapmap];0.91[MKK][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13322794	0.83[CEU][hapmap]
rs1549829	0.89[CEU][hapmap]
rs1554120	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs17290219	0.89[CEU][hapmap]
rs2141630	0.85[CEU][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2567325	0.94[CEU][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2700470	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4680158	0.85[CHD][hapmap]
rs6440722	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6792089	0.82[CEU][hapmap]
rs9818251	0.84[CEU][hapmap]
rs9836053	0.89[CEU][hapmap]
rs9854126	0.84[CEU][hapmap]
rs9871624	0.89[CEU][hapmap]
rs9876268	0.82[CEU][hapmap]
rs9881116	0.84[CEU][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	nsv460894	chr3:150770614-151095093	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv592045	chr3:150770614-151095093	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	esv2757897	chr3:150791625-150957485	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv2759188	chr3:150791625-150957485	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1920397	MME	cis	parietal	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150878000-150946000	Weak transcription	Placenta	Placenta
2	chr3:150928200-150936000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr3:150928800-150943800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:150928800-150946200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr3:150928800-150952800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:150928800-150953000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:150929000-150934400	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr3:150929000-150935000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr3:150929000-150938200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr3:150929000-150943200	Weak transcription	Psoas Muscle	Psoas
11	chr3:150929000-150945200	Weak transcription	Primary B cells from peripheral blood	blood
12	chr3:150929200-150935000	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr3:150929200-150938000	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr3:150929200-150945400	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr3:150929600-150939200	Weak transcription	Primary hematopoietic stem cells	blood
16	chr3:150929800-150935200	Weak transcription	Liver	Liver
17	chr3:150931400-150936000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr3:150932200-150934600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr3:150932200-150935000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr3:150932200-150936800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr3:150932200-150942800	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr3:150932400-150937400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr3:150932400-150938200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr3:150932600-150934400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr3:150932600-150946200	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr3:150933200-150935600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr3:150933400-150934400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr3:150933400-150937200	Strong transcription	Primary B cells from cord blood	blood
29	chr3:150933400-150937600	Enhancers	NHDF-Ad	bronchial
30	chr3:150933400-150937800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr3:150933600-150934400	Enhancers	Fetal Heart	heart
32	chr3:150933600-150935400	Enhancers	Adipose Nuclei	Adipose
33	chr3:150933600-150937200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr3:150933600-150937400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr3:150933600-150937600	Enhancers	NH-A	brain
36	chr3:150933600-150937600	Enhancers	NHLF	lung
37	chr3:150933800-150934600	Weak transcription	Rectal Smooth Muscle	rectum
38	chr3:150933800-150935000	Weak transcription	Left Ventricle	heart
39	chr3:150933800-150936800	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr3:150934000-150935400	Enhancers	Brain Anterior Caudate	brain
41	chr3:150934200-150934600	Enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr3:150934200-150935400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr3:150934200-150935600	Enhancers	Muscle Satellite Cultured Cells	--
44	chr3:150934200-150937400	Enhancers	Osteobl	bone

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