Variant report

Variant	rs4416499
Chromosome Location	chr4:79401728-79401729
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:79400879..79403380-chr4:79405475..79407306,2	K562	blood:
2	chr4:79393300..79397628-chr4:79398906..79402116,3	K562	blood:

Extended variants
information (count: 104 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs10023714	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10518200	0.87[EUR][1000 genomes]
rs11098197	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11098208	0.87[EUR][1000 genomes]
rs11721380	0.87[EUR][1000 genomes]
rs11722061	0.87[EUR][1000 genomes]
rs11723383	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs11723415	0.90[EUR][1000 genomes]
rs11724180	0.90[EUR][1000 genomes]
rs11725388	0.87[EUR][1000 genomes]
rs11725573	0.87[EUR][1000 genomes]
rs11727119	0.90[EUR][1000 genomes]
rs11727137	0.87[EUR][1000 genomes]
rs11728117	0.87[EUR][1000 genomes]
rs11728640	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11728758	0.88[EUR][1000 genomes]
rs11728817	0.88[EUR][1000 genomes]
rs11729604	0.87[EUR][1000 genomes]
rs11729705	0.88[EUR][1000 genomes]
rs11730601	0.87[EUR][1000 genomes]
rs11730636	0.87[EUR][1000 genomes]
rs11730668	0.87[EUR][1000 genomes]
rs11731012	0.87[EUR][1000 genomes]
rs11731074	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11731315	0.87[EUR][1000 genomes]
rs11731480	0.87[EUR][1000 genomes]
rs11731575	0.87[EUR][1000 genomes]
rs11733290	0.87[EUR][1000 genomes]
rs11733471	0.87[EUR][1000 genomes]
rs11736504	0.87[EUR][1000 genomes]
rs11933630	0.87[EUR][1000 genomes]
rs11939230	0.88[EUR][1000 genomes]
rs11939289	0.88[EUR][1000 genomes]
rs11940228	0.88[EUR][1000 genomes]
rs11941299	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11943426	0.88[EUR][1000 genomes]
rs11944743	1.00[CHD][hapmap]
rs13101600	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1353527	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1484332	1.00[CHD][hapmap]
rs1496600	0.88[EUR][1000 genomes]
rs1496603	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1496604	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17003235	0.83[EUR][1000 genomes]
rs17427362	0.83[EUR][1000 genomes]
rs17429053	0.92[EUR][1000 genomes]
rs17429432	0.88[EUR][1000 genomes]
rs17429467	0.88[EUR][1000 genomes]
rs17429649	0.88[EUR][1000 genomes]
rs17429670	0.88[EUR][1000 genomes]
rs17429718	0.88[EUR][1000 genomes]
rs17429816	0.87[EUR][1000 genomes]
rs17429963	0.87[EUR][1000 genomes]
rs17430075	0.87[EUR][1000 genomes]
rs17430137	0.87[EUR][1000 genomes]
rs17430229	0.87[EUR][1000 genomes]
rs17430243	0.87[EUR][1000 genomes]
rs17430334	0.87[EUR][1000 genomes]
rs17469341	1.00[CEU][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs17469981	0.88[EUR][1000 genomes]
rs17470002	0.87[EUR][1000 genomes]
rs17470023	0.87[EUR][1000 genomes]
rs17470072	0.87[EUR][1000 genomes]
rs17470303	0.87[EUR][1000 genomes]
rs17470490	0.87[EUR][1000 genomes]
rs17470553	0.87[EUR][1000 genomes]
rs17470609	0.87[EUR][1000 genomes]
rs17470811	0.87[EUR][1000 genomes]
rs17481799	0.87[EUR][1000 genomes]
rs1826845	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28568377	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28694126	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34435856	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35933858	0.87[EUR][1000 genomes]
rs4975129	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4975130	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55849455	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56681862	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs57325795	0.89[EUR][1000 genomes]
rs57356999	0.87[EUR][1000 genomes]
rs57558056	0.87[EUR][1000 genomes]
rs57771713	0.87[EUR][1000 genomes]
rs59347621	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59373877	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59658562	0.87[EUR][1000 genomes]
rs60144489	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60253739	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60805155	0.86[EUR][1000 genomes]
rs60991776	0.89[EUR][1000 genomes]
rs61185935	0.87[EUR][1000 genomes]
rs6817408	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6819837	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6825278	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6827590	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6846802	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6850657	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7436657	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7660569	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7686157	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs931603	0.87[EUR][1000 genomes]
rs931605	0.87[EUR][1000 genomes]
rs931607	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534024	chr4:78785189-79437403	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1009633	chr4:78887573-79652236	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4416499	PSTPIP1	trans	cerebellum	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79343200-79431800	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr4:79363200-79409800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr4:79363400-79455200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr4:79363800-79464200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:79365600-79406400	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr4:79366200-79408200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr4:79376200-79411600	Weak transcription	Fetal Stomach	stomach
8	chr4:79378600-79455800	Weak transcription	Right Ventricle	heart
9	chr4:79384600-79405400	Strong transcription	H1 Cell Line	embryonic stem cell
10	chr4:79384800-79405000	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr4:79384800-79405600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
12	chr4:79385000-79467400	Weak transcription	Fetal Brain Male	brain
13	chr4:79388200-79405000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr4:79391000-79405600	Weak transcription	Fetal Heart	heart
15	chr4:79391600-79406800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr4:79393000-79402200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr4:79393800-79467200	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr4:79394200-79402000	Weak transcription	HSMMtube	muscle
19	chr4:79396200-79406000	Strong transcription	HepG2	liver
20	chr4:79396800-79410000	Weak transcription	Pancreas	Pancrea
21	chr4:79398000-79409400	Weak transcription	Fetal Lung	lung
22	chr4:79398400-79405400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr4:79398400-79405800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr4:79398600-79403800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr4:79398600-79404600	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr4:79398800-79404000	Strong transcription	Fetal Intestine Small	intestine
27	chr4:79399000-79402000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr4:79399000-79402000	Weak transcription	NHLF	lung
29	chr4:79399000-79402600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr4:79399200-79401800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr4:79399200-79401800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr4:79399200-79402800	Weak transcription	Left Ventricle	heart
33	chr4:79399200-79404000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr4:79399200-79409800	Weak transcription	Aorta	Aorta
35	chr4:79399200-79410000	Weak transcription	Esophagus	oesophagus
36	chr4:79399400-79409800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr4:79400200-79403800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr4:79400600-79403600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr4:79400600-79403800	Strong transcription	Fetal Intestine Large	intestine
40	chr4:79400800-79403800	Strong transcription	Fetal Kidney	kidney
41	chr4:79400800-79404400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr4:79401000-79402600	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr4:79401000-79467200	Weak transcription	Psoas Muscle	Psoas
44	chr4:79401200-79404000	Enhancers	NHDF-Ad	bronchial
45	chr4:79401400-79402000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
46	chr4:79401400-79402000	Enhancers	Placenta Amnion	Placenta Amnion
47	chr4:79401600-79401800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr4:79401600-79402000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr4:79401600-79403000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr4:79401600-79403200	Enhancers	Muscle Satellite Cultured Cells	--

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