Variant report

Variant	rs1378658
Chromosome Location	chr3:160476232-160476233
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:160475234..160478424-chr3:160481295..160484751,3	MCF-7	breast:
2	chr3:160475604..160477135-chr3:160498622..160500263,2	K562	blood:
3	chr3:160475052..160477817-chr3:160492377..160494723,2	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10513553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12487861	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12637633	0.85[AMR][1000 genomes]
rs13080397	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs1378657	0.84[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap]
rs1455869	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1598495	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1829716	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1851378	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs1902282	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1915929	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2049214	0.83[ASN][1000 genomes]
rs2049215	0.83[ASN][1000 genomes]
rs4256178	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs6775743	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.90[YRI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6794047	0.83[ASN][1000 genomes]
rs718757	0.84[CEU][hapmap];0.96[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap]
rs722871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7618640	0.84[ASN][1000 genomes]
rs7618832	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7630250	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7648363	0.87[CEU][hapmap]
rs779058	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs972909	0.83[ASN][1000 genomes]
rs9814394	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9815499	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9824439	0.81[EUR][1000 genomes]
rs9833075	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs9866566	0.84[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap]
rs9868489	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160471800-160476600	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr3:160472000-160477800	Active TSS	Brain Angular Gyrus	brain
3	chr3:160472000-160477800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
4	chr3:160472200-160477400	Active TSS	Fetal Brain Female	brain
5	chr3:160472200-160477800	Active TSS	Duodenum Smooth Muscle	Duodenum
6	chr3:160474200-160476800	Flanking Active TSS	Dnd41	blood
7	chr3:160475200-160476400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr3:160475200-160476400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr3:160475400-160477200	Active TSS	Stomach Smooth Muscle	stomach
10	chr3:160475600-160476600	Active TSS	Skeletal Muscle Male	skeletal muscle
11	chr3:160475600-160477600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr3:160475600-160477600	Enhancers	Stomach Mucosa	stomach
13	chr3:160475600-160478200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr3:160475600-160478800	Active TSS	Brain Inferior Temporal Lobe	brain
15	chr3:160475800-160476400	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr3:160475800-160476400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr3:160475800-160476400	Active TSS	Hela-S3	cervix
18	chr3:160475800-160477000	Active TSS	HUES48 Cell Line	embryonic stem cell
19	chr3:160475800-160477600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr3:160475800-160497200	Weak transcription	Left Ventricle	heart
21	chr3:160476000-160476400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
22	chr3:160476000-160476400	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr3:160476000-160476600	Active TSS	iPS-20b Cell Line	embryonic stem cell
24	chr3:160476000-160476800	Enhancers	Brain Hippocampus Middle	brain
25	chr3:160476000-160477000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr3:160476000-160477000	Weak transcription	Brain Cingulate Gyrus	brain
27	chr3:160476000-160477000	Weak transcription	Brain Substantia Nigra	brain
28	chr3:160476000-160477200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr3:160476000-160477200	Weak transcription	Adipose Nuclei	Adipose
30	chr3:160476000-160477200	Active TSS	Fetal Brain Male	brain
31	chr3:160476000-160477400	Enhancers	Fetal Heart	heart
32	chr3:160476000-160477600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr3:160476000-160477600	Active TSS	Brain Anterior Caudate	brain
34	chr3:160476000-160478200	Enhancers	Colon Smooth Muscle	Colon
35	chr3:160476000-160480800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr3:160476000-160496400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr3:160476200-160476400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr3:160476200-160476400	Enhancers	HUES64 Cell Line	embryonic stem cell
39	chr3:160476200-160476400	Active TSS	Brain Germinal Matrix	brain
40	chr3:160476200-160477000	Weak transcription	Psoas Muscle	Psoas
41	chr3:160476200-160477200	Active TSS	Skeletal Muscle Female	skeletal muscle
42	chr3:160476200-160477400	Enhancers	Primary T cells from cord blood	blood
43	chr3:160476200-160479200	Weak transcription	Primary neutrophils fromperipheralblood	blood

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