Variant report

Variant	rs1345868
Chromosome Location	chr16:71669624-71669625
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr16:71669503-71669835	HL-60	blood:	n/a	n/a
2	EGR1	chr16:71669588-71669801	K562	blood:	n/a	n/a
3	SPI1	chr16:71669490-71669746	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:71668341..71670182-chr16:71677520..71679473,2	MCF-7	breast:
2	chr16:71659335..71662004-chr16:71667877..71670803,3	MCF-7	breast:
3	chr16:71668579..71670328-chr16:71676094..71677931,2	MCF-7	breast:

Variant related genes	Relation type
MARVELD3	TF binding region
ENSG00000140832	Chromatin interaction
ENSG00000260593	Chromatin interaction

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

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

rs_ID	r²[population]
rs10500560	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1056303	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11639902	1.00[ASW][hapmap];0.86[LWK][hapmap];0.83[MKK][hapmap];0.88[YRI][hapmap]
rs11640830	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11641967	1.00[CHB][hapmap]
rs11642529	1.00[JPT][hapmap]
rs11648483	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11670	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11861296	0.96[GIH][hapmap];0.83[TSI][hapmap]
rs11861513	0.82[CHB][hapmap];0.85[CHD][hapmap]
rs12445161	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12446005	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12448022	1.00[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12919271	0.81[EUR][1000 genomes]
rs12924631	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12928939	0.90[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs17345313	0.82[CHB][hapmap]
rs34028112	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34358623	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34680964	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34731378	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61733127	0.85[ASN][1000 genomes]
rs61753635	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71403864	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7185575	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7190257	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7192860	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7197104	0.80[EUR][1000 genomes]
rs7202840	0.90[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs7205340	0.93[ASW][hapmap];0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.93[MEX][hapmap];0.88[TSI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8046629	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs8049163	1.00[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8051878	0.90[CEU][hapmap];1.00[JPT][hapmap]
rs8053623	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[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	esv3347477	chr16:71555148-71985177	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv1063338	chr16:71612346-71752968	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv962218	chr16:71645202-71727606	Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1345868	PHLPP2	cis	cerebellum	SCAN
rs1345868	PHLPP2	cis	lymphoblastoid	seeQTL

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71661000-71671000	Weak transcription	Right Atrium	heart
2	chr16:71661000-71674200	Weak transcription	Gastric	stomach
3	chr16:71661800-71682000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr16:71662000-71674200	Weak transcription	Lung	lung
5	chr16:71662200-71671200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr16:71662600-71682000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr16:71662800-71673600	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr16:71663000-71670800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr16:71663200-71670000	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr16:71663200-71670600	Weak transcription	Osteobl	bone
11	chr16:71663200-71670800	Weak transcription	Ovary	ovary
12	chr16:71663200-71671000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr16:71663200-71673800	Weak transcription	Brain Hippocampus Middle	brain
14	chr16:71663200-71676800	Weak transcription	Fetal Kidney	kidney
15	chr16:71663400-71670000	Strong transcription	H1 Cell Line	embryonic stem cell
16	chr16:71663400-71674200	Weak transcription	Adipose Nuclei	Adipose
17	chr16:71663400-71674200	Weak transcription	Aorta	Aorta
18	chr16:71663400-71674400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr16:71663400-71674400	Weak transcription	Esophagus	oesophagus
20	chr16:71663400-71678400	Weak transcription	Fetal Lung	lung
21	chr16:71663600-71686600	Weak transcription	Small Intestine	intestine
22	chr16:71663800-71669800	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr16:71663800-71673800	Weak transcription	Stomach Smooth Muscle	stomach
24	chr16:71663800-71674200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr16:71663800-71680600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr16:71663800-71681400	Weak transcription	Left Ventricle	heart
27	chr16:71663800-71681400	Weak transcription	HepG2	liver
28	chr16:71664000-71671000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr16:71664200-71670400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr16:71664600-71682800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr16:71665000-71671000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr16:71665200-71673000	Strong transcription	Fetal Intestine Large	intestine
33	chr16:71665200-71673800	Weak transcription	Liver	Liver
34	chr16:71665200-71674200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr16:71665200-71682800	Weak transcription	HMEC	breast
36	chr16:71665400-71674200	Weak transcription	Brain Germinal Matrix	brain
37	chr16:71666000-71670000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr16:71666200-71671000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr16:71666200-71671000	Weak transcription	Fetal Heart	heart
40	chr16:71666200-71674200	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr16:71666400-71671000	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr16:71667000-71672000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr16:71667600-71669800	Strong transcription	Sigmoid Colon	Sigmoid Colon
44	chr16:71668000-71673800	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr16:71668000-71674200	Weak transcription	Fetal Brain Female	brain
46	chr16:71668000-71703000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr16:71668200-71681800	Weak transcription	Spleen	Spleen
48	chr16:71668600-71670800	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr16:71668600-71670800	Weak transcription	Duodenum Mucosa	Duodenum
50	chr16:71668600-71671000	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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