Variant report

Variant	rs722871
Chromosome Location	chr3:160499588-160499589
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	chr3:160471430..160473730-chr3:160499271..160501007,2	MCF-7	breast:
2	chr3:160475604..160477135-chr3:160498622..160500263,2	K562	blood:

Variant related genes	Relation type
ENSG00000163590	Chromatin interaction
ENSG00000260572	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10513553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12487861	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12637633	0.82[AMR][1000 genomes]
rs13080397	0.86[CEU][hapmap];0.82[GIH][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs1378654	0.85[ASN][1000 genomes]
rs1378657	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1378658	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]
rs1455869	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.93[YRI][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1598495	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16831457	0.86[YRI][hapmap]
rs1829716	0.89[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.80[MEX][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1851378	0.89[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs1902282	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1915929	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2049214	0.89[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2049215	0.87[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs4256178	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs6775743	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6794047	0.86[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs718757	0.88[ASW][hapmap];0.83[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.96[YRI][hapmap]
rs7618832	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7630250	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7633401	0.82[YRI][hapmap]
rs7648363	0.86[CEU][hapmap];0.81[JPT][hapmap]
rs779058	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs972909	0.89[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs9809208	0.80[JPT][hapmap]
rs9810290	0.80[JPT][hapmap]
rs9814394	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9815499	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9824439	0.81[EUR][1000 genomes]
rs9833075	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs9866566	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.80[ASN][1000 genomes]
rs9868489	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
2	nsv1009249	chr3:160496237-160627378	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv536780	chr3:160496237-160627378	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs722871	PPM1L	cis	cerebellum	SCAN
rs722871	IFT80	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160487200-160502200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr3:160495000-160502600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:160496200-160501000	Enhancers	Colon Smooth Muscle	Colon
4	chr3:160496400-160499600	Enhancers	Psoas Muscle	Psoas
5	chr3:160496400-160499600	Enhancers	Stomach Smooth Muscle	stomach
6	chr3:160496600-160503400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr3:160496800-160501600	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr3:160497000-160499600	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr3:160497200-160499600	Enhancers	Monocytes-CD14+_RO01746	blood
10	chr3:160497200-160502000	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr3:160498200-160499800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr3:160498200-160500400	Enhancers	Rectal Smooth Muscle	rectum
13	chr3:160498400-160522600	Weak transcription	Right Ventricle	heart
14	chr3:160498600-160499600	Weak transcription	Stomach Mucosa	stomach
15	chr3:160498600-160499800	Weak transcription	Brain Substantia Nigra	brain
16	chr3:160498600-160502600	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr3:160498600-160502600	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr3:160498800-160500000	Enhancers	Pancreatic Islets	Pancreatic Islet
19	chr3:160499000-160499600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
20	chr3:160499000-160499800	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr3:160499000-160500000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr3:160499000-160500400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:160499200-160499600	Enhancers	Brain Anterior Caudate	brain
24	chr3:160499200-160500200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr3:160499400-160499600	Enhancers	Brain Angular Gyrus	brain
26	chr3:160499400-160499600	Enhancers	Left Ventricle	heart
27	chr3:160499400-160499600	Enhancers	Small Intestine	intestine
28	chr3:160499400-160500000	Enhancers	Brain Cingulate Gyrus	brain
29	chr3:160499400-160500200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr3:160499400-160502400	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr3:160499400-160502600	Weak transcription	Skeletal Muscle Male	skeletal muscle

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