Variant report

Variant	rs17301853
Chromosome Location	chr1:174552811-174552812
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1013769	0.83[GIH][hapmap]
rs10494492	0.81[GIH][hapmap]
rs10798315	0.83[GIH][hapmap]
rs10912821	0.83[GIH][hapmap]
rs10912829	0.83[GIH][hapmap]
rs11806996	0.83[GIH][hapmap]
rs12076548	0.83[GIH][hapmap]
rs12079334	0.83[GIH][hapmap]
rs1474575	0.83[GIH][hapmap]
rs1622802	0.83[GIH][hapmap]
rs17301125	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17373189	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17842157	0.83[GIH][hapmap]
rs1793292	0.83[GIH][hapmap]
rs193082	0.83[GIH][hapmap]
rs2146564	0.83[GIH][hapmap]
rs2760057	0.83[GIH][hapmap]
rs2771401	0.83[GIH][hapmap]
rs332767	0.83[GIH][hapmap]
rs332768	0.83[GIH][hapmap]
rs332779	0.83[GIH][hapmap]
rs332781	0.83[GIH][hapmap]
rs332786	0.83[GIH][hapmap]
rs333422	0.83[GIH][hapmap]
rs333436	0.83[GIH][hapmap]
rs34409674	0.83[GIH][hapmap]
rs3862941	0.83[GIH][hapmap]
rs3862942	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3920486	0.83[GIH][hapmap]
rs411665	0.83[GIH][hapmap]
rs458242	0.83[GIH][hapmap]
rs4615901	0.83[GIH][hapmap]
rs464635	0.83[GIH][hapmap]
rs4651114	0.83[GIH][hapmap]
rs4652513	0.83[GIH][hapmap]
rs467437	0.83[GIH][hapmap]
rs6658917	1.00[AFR][1000 genomes]
rs6674239	0.83[GIH][hapmap]
rs6674797	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6682997	0.83[GIH][hapmap]
rs6689327	0.82[GIH][hapmap]
rs6696465	0.83[GIH][hapmap]
rs7411689	1.00[AFR][1000 genomes]
rs764918	0.90[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014637	chr1:174265631-174826765	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv535208	chr1:174265631-174826765	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1014753	chr1:174271770-174694838	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv872555	chr1:174343705-174565720	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	esv2755184	chr1:174388343-174970343	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
6	nsv1007667	chr1:174438778-174556953	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv999295	chr1:174457532-174596961	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv534381	chr1:174468168-174656796	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	esv2757762	chr1:174469281-174569776	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
10	esv2758979	chr1:174469281-174569776	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv548196	chr1:174525135-174559121	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
12	nsv947553	chr1:174548435-174554898	ZNF genes & repeats Weak transcription Enhancers Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
13	esv2762198	chr1:174552605-174559182	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

Variant related diseases (count:2)

Disease	PMID	Source
Migraine - clinic-based	23793025	GWAS catalog
Migraine without aura	23793025	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17301853	MRPS14	Cis_1M	lymphoblastoid	RTeQTL
rs17301853	RC3H1	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174545200-174555800	Weak transcription	Psoas Muscle	Psoas
2	chr1:174546000-174573000	Weak transcription	Left Ventricle	heart
3	chr1:174546200-174556800	Weak transcription	Primary B cells from cord blood	blood
4	chr1:174547200-174554400	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr1:174552200-174554400	Weak transcription	Primary B cells from peripheral blood	blood
6	chr1:174552800-174554600	Weak transcription	GM12878-XiMat	blood

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