Variant report

Variant	rs17166614
Chromosome Location	chr7:13071986-13071987
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:13067871..13070074-chr7:13070910..13073106,2	K562	blood:

Extended variants
information (count: 102 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10488243	0.89[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10950428	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10950431	0.82[AMR][1000 genomes]
rs10950432	0.82[AMR][1000 genomes]
rs10950433	0.82[AMR][1000 genomes]
rs10950434	0.82[AMR][1000 genomes]
rs11975327	1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs12056168	0.82[AMR][1000 genomes]
rs12112648	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12113090	0.91[JPT][hapmap]
rs12530565	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12530643	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12530651	0.90[ASN][1000 genomes]
rs12531362	0.85[JPT][hapmap]
rs12531363	0.91[JPT][hapmap]
rs12532653	0.90[ASN][1000 genomes]
rs12534513	0.81[AMR][1000 genomes]
rs12534537	0.92[ASN][1000 genomes]
rs12534546	0.81[AMR][1000 genomes]
rs12537378	0.87[ASN][1000 genomes]
rs12537712	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12539699	0.81[AMR][1000 genomes]
rs12671480	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12672647	0.98[ASN][1000 genomes]
rs17166605	0.96[ASN][1000 genomes]
rs17166608	0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs17166610	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17166612	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs17166626	0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs17166643	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17166651	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs17166653	0.88[GIH][hapmap]
rs17166655	0.81[CHD][hapmap];0.88[GIH][hapmap]
rs17166658	0.81[CHD][hapmap];0.88[GIH][hapmap]
rs17166671	0.95[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs17166673	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17166683	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17166711	0.81[AMR][1000 genomes]
rs17166756	0.91[JPT][hapmap]
rs1861237	0.89[ASN][1000 genomes]
rs1981639	0.91[JPT][hapmap]
rs2110650	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2191043	0.83[JPT][hapmap]
rs2215950	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34125302	0.90[ASN][1000 genomes]
rs4236278	0.91[JPT][hapmap]
rs4636097	0.95[ASN][1000 genomes]
rs4719347	1.00[ASN][1000 genomes]
rs4721177	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs55957561	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57459966	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs58757383	0.85[EUR][1000 genomes]
rs59675898	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60020188	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs60345281	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60705466	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs61232028	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61639094	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6460997	0.81[AMR][1000 genomes]
rs6461007	0.89[CEU][hapmap];0.91[JPT][hapmap]
rs6950438	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6950752	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6956549	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6964875	0.90[JPT][hapmap]
rs6974627	0.91[JPT][hapmap]
rs6977552	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs73259988	0.90[ASN][1000 genomes]
rs73259991	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs73261908	0.96[ASN][1000 genomes]
rs73261911	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73261913	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73261923	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs73261936	0.94[ASN][1000 genomes]
rs73261954	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73261964	0.90[ASN][1000 genomes]
rs738052	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs763534	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7777911	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7778632	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7778887	0.81[AMR][1000 genomes]
rs7787998	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7788484	0.91[JPT][hapmap]
rs7789970	0.91[JPT][hapmap]
rs7790328	0.91[JPT][hapmap]
rs7790665	0.91[JPT][hapmap]
rs7790770	0.91[JPT][hapmap]
rs7793289	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7793573	0.82[AMR][1000 genomes]
rs7797104	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7809172	0.83[AMR][1000 genomes]
rs9639142	0.91[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932020	chr7:12676890-13239551	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv868830	chr7:12712753-13517417	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv606235	chr7:12781381-13205950	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1020568	chr7:12802640-13183737	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv464384	chr7:12907178-13077065	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv606238	chr7:12907178-13077065	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv1029771	chr7:12927648-13153855	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv538736	chr7:12927648-13153855	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv1026624	chr7:12963907-13123408	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1019173	chr7:13063854-13585360	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv538737	chr7:13063854-13585360	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17166614	ARL4A	cis	parietal	SCAN
rs17166614	TSPAN13	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:13069800-13072200	Weak transcription	Fetal Kidney	kidney
2	chr7:13070000-13075200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr7:13070800-13072400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr7:13070800-13072400	Enhancers	NHEK	skin
5	chr7:13070800-13072600	Enhancers	HMEC	breast
6	chr7:13070800-13074600	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr7:13071000-13072000	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr7:13071000-13072000	Enhancers	Hela-S3	cervix
9	chr7:13071200-13072600	Enhancers	H1 Cell Line	embryonic stem cell
10	chr7:13071200-13072600	Enhancers	HepG2	liver
11	chr7:13071200-13073400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr7:13071200-13075200	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr7:13071400-13072000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr7:13071400-13073600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr7:13071400-13075000	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr7:13071600-13072000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr7:13071600-13072200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr7:13071600-13072200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr7:13071600-13072600	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr7:13071600-13072800	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr7:13071600-13073000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
22	chr7:13071600-13074600	Enhancers	HUES48 Cell Line	embryonic stem cell
23	chr7:13071800-13072800	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr7:13071800-13073800	Enhancers	Rectal Smooth Muscle	rectum
25	chr7:13071800-13073800	Enhancers	A549	lung
26	chr7:13071800-13075400	Enhancers	iPS-15b Cell Line	embryonic stem cell

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