Variant report

Variant	rs1829716
Chromosome Location	chr3:160477861-160477862
allele	A/G
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	chr3:160471736..160473920-chr3:160477705..160480037,3	K562	blood:
3	chr3:160471123..160476793-chr3:160477705..160482988,8	K562	blood:

Variant related genes	Relation type
ENSG00000163590	Chromatin interaction
ENSG00000260572	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10513553	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12486979	0.81[EUR][1000 genomes]
rs12487861	0.89[ASW][hapmap];0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.91[LWK][hapmap];0.80[MEX][hapmap];0.81[MKK][hapmap];0.96[YRI][hapmap]
rs13068380	0.88[EUR][1000 genomes]
rs1378654	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1378657	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes]
rs1378658	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]
rs1403048	0.83[EUR][1000 genomes]
rs1455869	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1598495	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16831457	0.86[YRI][hapmap]
rs1851378	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1902282	0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1915929	0.80[AFR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2049214	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2049215	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2886905	0.82[EUR][1000 genomes]
rs59542611	0.89[EUR][1000 genomes]
rs6775743	0.83[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.96[YRI][hapmap]
rs6781371	0.80[EUR][1000 genomes]
rs6794047	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6805905	0.82[EUR][1000 genomes]
rs718757	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.93[LWK][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.89[EUR][1000 genomes]
rs722871	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]
rs7618640	0.84[ASN][1000 genomes]
rs7618832	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7630250	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7633401	0.82[YRI][hapmap]
rs7634342	0.82[EUR][1000 genomes]
rs7640348	0.80[EUR][1000 genomes]
rs7642371	0.82[EUR][1000 genomes]
rs7643513	0.83[EUR][1000 genomes]
rs779058	0.83[ASN][1000 genomes]
rs959960	0.80[EUR][1000 genomes]
rs972909	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9814394	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9815499	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9833075	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9866566	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.89[EUR][1000 genomes]
rs9868489	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.81[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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1829716	IFT80	cis	parietal	SCAN
rs1829716	PPM1L	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160475600-160478200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr3:160475600-160478800	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr3:160475800-160497200	Weak transcription	Left Ventricle	heart
4	chr3:160476000-160478200	Enhancers	Colon Smooth Muscle	Colon
5	chr3:160476000-160480800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:160476000-160496400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr3:160476200-160479200	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr3:160477200-160479600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:160477400-160478000	Enhancers	Brain Germinal Matrix	brain
10	chr3:160477400-160478000	Enhancers	Psoas Muscle	Psoas
11	chr3:160477400-160478400	Enhancers	Fetal Brain Male	brain
12	chr3:160477400-160489600	Weak transcription	Fetal Heart	heart
13	chr3:160477600-160478000	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr3:160477600-160478000	Enhancers	Dnd41	blood
15	chr3:160477600-160478400	Active TSS	Stomach Smooth Muscle	stomach
16	chr3:160477600-160483000	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr3:160477600-160489800	Weak transcription	Brain Anterior Caudate	brain
18	chr3:160477600-160497000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr3:160477600-160498200	Weak transcription	Stomach Mucosa	stomach
20	chr3:160477800-160478000	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
21	chr3:160477800-160479200	Active TSS	Fetal Brain Female	brain
22	chr3:160477800-160485600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr3:160477800-160488200	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr3:160477800-160497800	Weak transcription	Brain Angular Gyrus	brain

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