Variant report

Variant	rs16978517
Chromosome Location	chr18:43610416-43610417
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	chr18:43605354..43607619-chr18:43610369..43613153,2	K562	blood:

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10468859	0.81[CHD][hapmap]
rs10468860	0.86[CHB][hapmap];0.80[JPT][hapmap];0.82[ASN][1000 genomes]
rs10468980	0.81[CHB][hapmap]
rs10502871	0.98[CHD][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs11082506	0.82[ASN][1000 genomes]
rs12604893	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12606939	0.87[ASN][1000 genomes]
rs12607686	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16978508	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16978509	0.85[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16978516	0.85[ASN][1000 genomes]
rs1837213	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3745001	0.85[CEU][hapmap];0.88[GIH][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs3897646	0.80[EUR][1000 genomes]
rs486424	1.00[CEU][hapmap];0.89[CHB][hapmap];0.88[JPT][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs488431	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4890310	0.86[ASN][1000 genomes]
rs4890612	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4890613	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4890614	0.98[CHD][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs4890615	0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs55966192	0.84[ASN][1000 genomes]
rs567504	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs568448	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57141604	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs593664	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.82[TSI][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs596415	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs610186	0.81[ASN][1000 genomes]
rs61423911	0.82[ASN][1000 genomes]
rs6507659	0.91[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs6507660	0.81[ASN][1000 genomes]
rs6507661	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6507662	0.98[CHD][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs654466	0.98[CHD][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs68061103	0.86[ASN][1000 genomes]
rs687526	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs688547	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7237813	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72642435	0.83[ASN][1000 genomes]
rs8097830	0.93[CHD][hapmap];0.83[ASN][1000 genomes]
rs9675392	0.90[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap]

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	nsv1064882	chr18:43558343-43687674	Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv543693	chr18:43558343-43687674	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv1062024	chr18:43589516-43749410	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv543694	chr18:43589516-43749410	Strong transcription Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16978517	PSTPIP2	cis	lymphoblastoid	seeQTL

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:43571400-43622000	Weak transcription	Gastric	stomach
2	chr18:43599600-43610600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr18:43601000-43619000	Weak transcription	K562	blood
4	chr18:43608000-43614000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr18:43608600-43613600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr18:43608600-43615600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr18:43608600-43616400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr18:43608600-43616400	Weak transcription	Psoas Muscle	Psoas
9	chr18:43608600-43617400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr18:43608600-43619000	Weak transcription	Right Ventricle	heart
11	chr18:43608600-43651000	Weak transcription	Esophagus	oesophagus
12	chr18:43608800-43610600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr18:43608800-43610600	Weak transcription	HMEC	breast
14	chr18:43608800-43610600	Weak transcription	NHEK	skin
15	chr18:43608800-43613600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr18:43608800-43613800	Weak transcription	Primary hematopoietic stem cells	blood
17	chr18:43608800-43614000	Weak transcription	Osteobl	bone
18	chr18:43608800-43616400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr18:43608800-43619800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr18:43608800-43620000	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr18:43608800-43620400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr18:43608800-43620600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr18:43608800-43620600	Weak transcription	Placenta	Placenta
24	chr18:43608800-43631800	Weak transcription	NHLF	lung
25	chr18:43608800-43632000	Weak transcription	Aorta	Aorta
26	chr18:43609000-43610600	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr18:43609000-43611000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr18:43609000-43613800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr18:43609000-43617400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr18:43609000-43617400	Weak transcription	Liver	Liver
31	chr18:43609000-43617600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr18:43609000-43618400	Weak transcription	Primary T cells from cord blood	blood
33	chr18:43609000-43619600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr18:43609000-43619800	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr18:43609000-43620000	Weak transcription	Lung	lung
36	chr18:43609000-43620000	Weak transcription	Ovary	ovary
37	chr18:43609000-43622200	Weak transcription	Brain Hippocampus Middle	brain
38	chr18:43609000-43622200	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr18:43609000-43622200	Weak transcription	Stomach Smooth Muscle	stomach
40	chr18:43609000-43622200	Weak transcription	Thymus	Thymus
41	chr18:43609000-43631800	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr18:43609000-43631800	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr18:43609200-43610600	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr18:43609200-43611200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr18:43609200-43612000	Enhancers	Primary neutrophils fromperipheralblood	blood
46	chr18:43609200-43615600	Weak transcription	Spleen	Spleen
47	chr18:43609200-43620000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr18:43609200-43620200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr18:43609600-43610600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr18:43609600-43620000	Weak transcription	Fetal Intestine Large	intestine

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