Variant report

Variant	rs1388628
Chromosome Location	chr3:151045246-151045247
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:151029737..151031573-chr3:151044175..151046393,2	MCF-7	breast:
2	chr3:151008127..151009123-chr3:151045003..151046087,3	MCF-7	breast:
3	chr3:151021234..151025100-chr3:151041293..151045950,7	MCF-7	breast:
4	chr3:150945207..150946162-chr3:151045062..151046047,6	K562	blood:
5	chr3:150945279..150946102-chr3:151045158..151045936,2	MCF-7	breast:
6	chr3:151032337..151036170-chr3:151042057..151045470,4	MCF-7	breast:
7	chr3:151008218..151009783-chr3:151044914..151046119,9	MCF-7	breast:
8	chr3:151033641..151035853-chr3:151044142..151046293,2	MCF-7	breast:
9	chr3:151021027..151023183-chr3:151044316..151046639,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000144893	Chromatin interaction
ENSG00000138271	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1125541	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11708287	0.81[JPT][hapmap]
rs11715892	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11717634	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11717955	0.81[CEU][hapmap]
rs12487835	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12492699	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12494865	0.91[CEU][hapmap]
rs13088531	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13090321	0.84[EUR][1000 genomes]
rs1352886	0.85[CEU][hapmap]
rs1388627	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16863323	0.90[CEU][hapmap]
rs16863334	0.86[CEU][hapmap]
rs16863336	0.84[CEU][hapmap]
rs16863339	1.00[YRI][hapmap]
rs3971192	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4076581	0.85[CEU][hapmap]
rs41399847	0.82[JPT][hapmap]
rs4679794	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6793061	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[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	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	esv2754555	chr3:150968302-151054302	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv829757	chr3:151044880-151226442	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:151038800-151046400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr3:151042600-151046200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:151044200-151045400	Transcr. at gene 5' and 3'	Primary neutrophils fromperipheralblood	blood
4	chr3:151044400-151045600	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr3:151044400-151047000	Active TSS	Brain Hippocampus Middle	brain
6	chr3:151044600-151046200	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
7	chr3:151045000-151045400	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr3:151045000-151045400	Transcr. at gene 5' and 3'	Primary monocytes fromperipheralblood	blood
9	chr3:151045000-151045400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr3:151045000-151045600	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr3:151045000-151045600	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr3:151045000-151045600	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr3:151045000-151045800	Active TSS	Primary B cells from cord blood	blood
14	chr3:151045000-151046000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr3:151045000-151046800	Flanking Active TSS	Adipose Nuclei	Adipose
16	chr3:151045000-151046800	Active TSS	Brain Cingulate Gyrus	brain
17	chr3:151045000-151046800	Active TSS	Brain Inferior Temporal Lobe	brain
18	chr3:151045000-151047200	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
19	chr3:151045000-151047200	Active TSS	Rectal Mucosa Donor 29	rectum
20	chr3:151045200-151045400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr3:151045200-151045400	Flanking Active TSS	Primary hematopoietic stem cells	blood
22	chr3:151045200-151045400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr3:151045200-151045400	Flanking Active TSS	Liver	Liver
24	chr3:151045200-151045400	Flanking Active TSS	Brain Angular Gyrus	brain
25	chr3:151045200-151045400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
26	chr3:151045200-151045400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr3:151045200-151045400	Enhancers	Hela-S3	cervix
28	chr3:151045200-151045600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr3:151045200-151046000	Enhancers	NHLF	lung
30	chr3:151045200-151046200	Enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr3:151045200-151046200	Enhancers	Brain Anterior Caudate	brain
32	chr3:151045200-151046200	Enhancers	HMEC	breast
33	chr3:151045200-151046200	Enhancers	NHEK	skin
34	chr3:151045200-151046600	Active TSS	Brain Substantia Nigra	brain
35	chr3:151045200-151046800	Active TSS	Duodenum Mucosa	Duodenum
36	chr3:151045200-151046800	Active TSS	Right Atrium	heart
37	chr3:151045200-151047000	Active TSS	Duodenum Smooth Muscle	Duodenum
38	chr3:151045200-151047600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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