Variant report

Variant	rs13117388
Chromosome Location	chr4:79173335-79173336
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 93 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10008653	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10010118	0.96[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10015504	0.82[ASN][1000 genomes]
rs10027981	0.84[ASN][1000 genomes]
rs10028695	0.80[ASN][1000 genomes]
rs1017649	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10223012	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10461146	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11730296	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11736213	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12500443	0.97[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12501798	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12502139	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12502685	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12502886	0.82[ASN][1000 genomes]
rs12504081	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12505633	0.80[AMR][1000 genomes]
rs12506036	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12506989	0.82[EUR][1000 genomes]
rs12510741	0.82[ASN][1000 genomes]
rs12511033	0.80[ASN][1000 genomes]
rs12511360	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12511808	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12511889	0.92[AMR][1000 genomes]
rs13107378	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13108102	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13114110	0.93[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs13136648	0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13138795	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1378239	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1454892	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1454898	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1454899	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1484344	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17455826	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1840391	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1840392	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1952399	0.83[ASN][1000 genomes]
rs2008786	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2124143	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2124144	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2168203	0.85[ASN][1000 genomes]
rs2198635	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28493765	0.84[ASN][1000 genomes]
rs2867012	0.84[ASN][1000 genomes]
rs28737438	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34321445	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34398622	0.82[ASN][1000 genomes]
rs34535077	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs345507	0.80[ASN][1000 genomes]
rs34595864	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34643532	0.86[AMR][1000 genomes]
rs35290872	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35291597	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35419939	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35683023	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35828300	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs41537644	0.86[AMR][1000 genomes]
rs4515188	0.83[AMR][1000 genomes]
rs4859918	0.82[ASN][1000 genomes]
rs4859920	0.82[ASN][1000 genomes]
rs4859923	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4859924	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs58101131	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62309861	0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62310017	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62310021	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62310023	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62310045	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6533565	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6533571	0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6815945	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6833721	0.82[CHB][hapmap]
rs6854043	0.96[CEU][hapmap];0.80[CHB][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6854207	0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6856362	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72657047	0.93[ASN][1000 genomes]
rs7656032	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7681247	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7686297	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7694740	0.82[ASN][1000 genomes]
rs7696792	0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7698625	0.90[EUR][1000 genomes]
rs9307359	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs943821	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs943822	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9762380	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9994502	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
3	nsv525530	chr4:79024524-79266563	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv1010782	chr4:79057839-79387207	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv829978	chr4:79144453-79291868	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13117388	THAP6	cis	parietal	SCAN
rs13117388	PARM1	cis	cerebellum	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79144200-79176000	Weak transcription	Psoas Muscle	Psoas
2	chr4:79144600-79179000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:79154400-79173600	Weak transcription	HepG2	liver
4	chr4:79163600-79173600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr4:79166600-79173400	Weak transcription	Fetal Intestine Large	intestine
6	chr4:79167800-79176000	Weak transcription	Esophagus	oesophagus
7	chr4:79169200-79186200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr4:79169200-79187400	Weak transcription	HSMMtube	muscle
9	chr4:79169600-79173800	Weak transcription	Fetal Kidney	kidney
10	chr4:79169600-79174000	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr4:79169600-79187800	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr4:79169800-79197400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr4:79169800-79213800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr4:79170200-79173400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr4:79170200-79174000	Weak transcription	Fetal Lung	lung
16	chr4:79170400-79186000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr4:79170600-79176200	Weak transcription	Fetal Heart	heart
18	chr4:79170800-79176000	Weak transcription	Pancreas	Pancrea
19	chr4:79171200-79173400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr4:79171400-79173400	Enhancers	iPS-18 Cell Line	embryonic stem cell
21	chr4:79172400-79174200	Enhancers	H1 Cell Line	embryonic stem cell
22	chr4:79172400-79175400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
23	chr4:79172400-79175800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr4:79172600-79173800	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr4:79172600-79175000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr4:79172600-79175000	ZNF genes & repeats	Fetal Intestine Small	intestine
27	chr4:79172600-79175200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr4:79172800-79173600	Enhancers	iPS-20b Cell Line	embryonic stem cell
29	chr4:79172800-79174400	Enhancers	H9 Cell Line	embryonic stem cell
30	chr4:79172800-79175400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
31	chr4:79173200-79173600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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