Variant report

Variant	rs7660569
Chromosome Location	chr4:79406069-79406070
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:79394966..79397409-chr4:79405823..79407629,2	K562	blood:
2	chr4:79400879..79403380-chr4:79405475..79407306,2	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	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10518200	0.86[EUR][1000 genomes]
rs11098197	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11098208	0.86[EUR][1000 genomes]
rs11721380	0.86[EUR][1000 genomes]
rs11722061	0.86[EUR][1000 genomes]
rs11723383	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs11723415	0.88[EUR][1000 genomes]
rs11724180	0.88[EUR][1000 genomes]
rs11725388	0.86[EUR][1000 genomes]
rs11725573	0.86[EUR][1000 genomes]
rs11727119	0.88[EUR][1000 genomes]
rs11727137	0.86[EUR][1000 genomes]
rs11728117	0.86[EUR][1000 genomes]
rs11728640	0.91[EUR][1000 genomes]
rs11728758	0.87[EUR][1000 genomes]
rs11728817	0.87[EUR][1000 genomes]
rs11729604	0.86[EUR][1000 genomes]
rs11729705	0.87[EUR][1000 genomes]
rs11730601	0.86[EUR][1000 genomes]
rs11730636	0.86[EUR][1000 genomes]
rs11730668	0.86[EUR][1000 genomes]
rs11731012	0.86[EUR][1000 genomes]
rs11731074	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11731315	0.86[EUR][1000 genomes]
rs11731480	0.86[EUR][1000 genomes]
rs11731575	0.86[EUR][1000 genomes]
rs11733290	0.85[EUR][1000 genomes]
rs11733471	0.86[EUR][1000 genomes]
rs11736504	0.86[EUR][1000 genomes]
rs11933630	0.85[EUR][1000 genomes]
rs11939230	0.87[EUR][1000 genomes]
rs11939289	0.87[EUR][1000 genomes]
rs11940228	0.87[EUR][1000 genomes]
rs11941299	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11943426	0.87[EUR][1000 genomes]
rs11944743	1.00[CHD][hapmap];0.80[TSI][hapmap]
rs13101600	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1353527	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1484332	1.00[CHD][hapmap];0.80[TSI][hapmap]
rs1496600	0.89[EUR][1000 genomes]
rs1496603	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1496604	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17003235	0.84[EUR][1000 genomes]
rs17427362	0.85[EUR][1000 genomes]
rs17429053	0.90[EUR][1000 genomes]
rs17429432	0.87[EUR][1000 genomes]
rs17429467	0.87[EUR][1000 genomes]
rs17429649	0.87[EUR][1000 genomes]
rs17429670	0.87[EUR][1000 genomes]
rs17429718	0.87[EUR][1000 genomes]
rs17429816	0.86[EUR][1000 genomes]
rs17429963	0.86[EUR][1000 genomes]
rs17430075	0.85[EUR][1000 genomes]
rs17430137	0.86[EUR][1000 genomes]
rs17430229	0.86[EUR][1000 genomes]
rs17430243	0.86[EUR][1000 genomes]
rs17430334	0.86[EUR][1000 genomes]
rs17469341	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs17469981	0.87[EUR][1000 genomes]
rs17470002	0.86[EUR][1000 genomes]
rs17470023	0.86[EUR][1000 genomes]
rs17470072	0.86[EUR][1000 genomes]
rs17470303	0.86[EUR][1000 genomes]
rs17470490	0.86[EUR][1000 genomes]
rs17470553	0.86[EUR][1000 genomes]
rs17470609	0.86[EUR][1000 genomes]
rs17470811	0.86[EUR][1000 genomes]
rs17481799	0.86[EUR][1000 genomes]
rs1826845	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28568377	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28694126	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34435856	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35933858	0.86[EUR][1000 genomes]
rs4416499	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4975129	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4975130	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55849455	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56681862	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57325795	0.88[EUR][1000 genomes]
rs57356999	0.86[EUR][1000 genomes]
rs57558056	0.86[EUR][1000 genomes]
rs57771713	0.86[EUR][1000 genomes]
rs59347621	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59373877	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs59658562	0.85[EUR][1000 genomes]
rs60144489	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60253739	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60805155	0.84[EUR][1000 genomes]
rs60991776	0.88[EUR][1000 genomes]
rs61185935	0.86[EUR][1000 genomes]
rs6817408	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6819837	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6825278	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6827590	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6846802	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6850657	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7436657	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7686157	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs931603	0.86[EUR][1000 genomes]
rs931605	0.86[EUR][1000 genomes]
rs931607	0.94[AMR][1000 genomes];1.00[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
rs7660569	PSTPIP1	trans	cerebellum	SCAN

Chromatin state (count:45 , 50 per page) page: 1

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	chr4:79385000-79467400	Weak transcription	Fetal Brain Male	brain
10	chr4:79391600-79406800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr4:79393800-79467200	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr4:79396800-79410000	Weak transcription	Pancreas	Pancrea
13	chr4:79398000-79409400	Weak transcription	Fetal Lung	lung
14	chr4:79399200-79409800	Weak transcription	Aorta	Aorta
15	chr4:79399200-79410000	Weak transcription	Esophagus	oesophagus
16	chr4:79399400-79409800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr4:79401000-79467200	Weak transcription	Psoas Muscle	Psoas
18	chr4:79402000-79427600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr4:79402400-79409600	Weak transcription	HSMMtube	muscle
20	chr4:79403000-79407600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr4:79403000-79420200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr4:79403200-79428000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr4:79403200-79449800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr4:79403600-79409800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr4:79403800-79406200	Weak transcription	Fetal Intestine Large	intestine
26	chr4:79403800-79407600	Weak transcription	Left Ventricle	heart
27	chr4:79403800-79409800	Weak transcription	Fetal Kidney	kidney
28	chr4:79403800-79411000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr4:79403800-79428000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr4:79404000-79409800	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr4:79404000-79427200	Weak transcription	Fetal Intestine Small	intestine
32	chr4:79404200-79450200	Weak transcription	HMEC	breast
33	chr4:79404400-79431800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr4:79404600-79409800	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr4:79405000-79406200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr4:79405000-79407400	Enhancers	K562	blood
37	chr4:79405000-79410000	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr4:79405400-79407000	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr4:79405400-79407400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr4:79405400-79408200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr4:79405600-79406800	Enhancers	Fetal Heart	heart
42	chr4:79405600-79408000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr4:79405800-79406800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr4:79406000-79408000	Weak transcription	NHDF-Ad	bronchial
45	chr4:79406000-79409800	Weak transcription	HepG2	liver

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