Variant report

Variant	rs344027
Chromosome Location	chr3:156468393-156468394
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:156467361..156469859-chr3:156528012..156530054,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000230457	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11914959	0.83[JPT][hapmap]
rs12497777	0.83[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs13063433	0.91[ASN][1000 genomes]
rs13068223	0.89[CEU][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13095806	0.85[EUR][1000 genomes]
rs13322900	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1367311	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs1560414	0.89[CEU][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs168247	0.85[CHB][hapmap];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs17380702	0.81[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs17380954	0.83[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs184695	0.92[CHB][hapmap]
rs193197	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs2321291	0.82[JPT][hapmap]
rs237250	0.82[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs34111024	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs343999	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs344003	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs344028	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs344034	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs344035	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs344067	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs345986	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs34901284	0.83[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs35161260	0.84[ASN][1000 genomes]
rs36126086	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs374341	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs386736	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9289971	0.83[CHB][hapmap]
rs9868587	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9871258	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9873307	0.87[ASN][1000 genomes]
rs9883439	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428745	chr3:156405054-156577840	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv877685	chr3:156444383-156611676	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs344027	Hs.54543	cis	multi-tissue	Pritchard

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156460000-156468400	Weak transcription	Pancreas	Pancrea
2	chr3:156466200-156470200	Enhancers	Fetal Muscle Leg	muscle
3	chr3:156466600-156469600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:156466800-156468400	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr3:156466800-156468400	Enhancers	iPS-20b Cell Line	embryonic stem cell
6	chr3:156466800-156468400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr3:156466800-156469000	Enhancers	H1 Cell Line	embryonic stem cell
8	chr3:156466800-156469000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr3:156466800-156469000	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr3:156466800-156469000	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr3:156466800-156469400	Enhancers	Brain Cingulate Gyrus	brain
12	chr3:156466800-156469600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
13	chr3:156466800-156469600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr3:156466800-156469600	Enhancers	Fetal Heart	heart
15	chr3:156466800-156469800	Enhancers	Fetal Kidney	kidney
16	chr3:156466800-156469800	Enhancers	Fetal Lung	lung
17	chr3:156466800-156471200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr3:156467000-156468400	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr3:156467000-156468400	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr3:156467000-156468400	Enhancers	NHLF	lung
21	chr3:156467000-156468600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr3:156467000-156469000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr3:156467000-156469200	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr3:156467000-156469400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr3:156467000-156469400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr3:156467000-156469600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr3:156467000-156469600	Enhancers	Fetal Muscle Trunk	muscle
28	chr3:156467000-156469800	Enhancers	Brain Substantia Nigra	brain
29	chr3:156467000-156470200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr3:156467000-156470200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr3:156467000-156470200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr3:156467200-156468400	Enhancers	iPS-15b Cell Line	embryonic stem cell
33	chr3:156467200-156468400	Enhancers	Osteobl	bone
34	chr3:156467200-156468600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr3:156467200-156468600	Enhancers	NHDF-Ad	bronchial
36	chr3:156467200-156469400	Enhancers	H9 Cell Line	embryonic stem cell
37	chr3:156467400-156469200	Enhancers	Brain Hippocampus Middle	brain
38	chr3:156467600-156468400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr3:156467600-156468400	Weak transcription	Fetal Intestine Small	intestine
40	chr3:156467600-156468600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr3:156467600-156470200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr3:156467800-156468400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr3:156467800-156469000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr3:156467800-156469400	Flanking Active TSS	HSMMtube	muscle
45	chr3:156467800-156469600	Enhancers	Brain Germinal Matrix	brain
46	chr3:156467800-156470000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
47	chr3:156467800-156470200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr3:156467800-156470200	Enhancers	Fetal Stomach	stomach
49	chr3:156468000-156468400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr3:156468000-156468600	Enhancers	Breast Myoepithelial Primary Cells	Breast

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