Variant report

Variant	rs2038025
Chromosome Location	chr1:174543850-174543851
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	chr1:174537431..174539369-chr1:174541884..174544062,2	K562	blood:
2	chr1:174537054..174539369-chr1:174541231..174544062,3	K562	blood:

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10158096	0.80[CHB][hapmap]
rs10218528	0.85[EUR][1000 genomes]
rs10494493	0.80[CHB][hapmap]
rs10753086	0.88[CEU][hapmap];0.87[MEX][hapmap]
rs10912773	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10912797	0.88[CEU][hapmap];0.87[MEX][hapmap]
rs10912807	0.88[CEU][hapmap];0.87[MEX][hapmap]
rs10912824	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11804941	0.88[CEU][hapmap];0.87[MEX][hapmap]
rs12060177	0.88[CEU][hapmap]
rs12074753	0.88[CEU][hapmap];0.87[MEX][hapmap]
rs12077622	0.88[CEU][hapmap];0.83[MEX][hapmap]
rs12084119	0.88[CEU][hapmap];0.87[MEX][hapmap]
rs12088073	0.88[CEU][hapmap];0.87[MEX][hapmap]
rs12094143	0.83[CEU][hapmap]
rs12564992	0.80[CHB][hapmap]
rs12565430	0.80[CHB][hapmap]
rs12568655	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.82[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1653626	0.88[CEU][hapmap];0.83[MEX][hapmap]
rs1653627	0.88[CEU][hapmap];0.87[MEX][hapmap]
rs16847257	0.80[CHB][hapmap]
rs16847402	0.80[CHB][hapmap]
rs170768	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1754351	0.88[CEU][hapmap];0.87[MEX][hapmap]
rs1793293	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1793319	0.82[EUR][1000 genomes]
rs2006197	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2049991	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2072758	0.80[CHB][hapmap]
rs332765	0.84[CEU][hapmap];0.83[MEX][hapmap]
rs332783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs332795	0.88[CEU][hapmap];0.87[MEX][hapmap]
rs332796	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs332799	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs333418	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3737651	0.88[CEU][hapmap];0.87[MEX][hapmap]
rs61826916	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6425279	0.92[CEU][hapmap];0.87[MEX][hapmap]
rs6425280	0.88[CEU][hapmap];0.87[MEX][hapmap]
rs6425281	0.88[CEU][hapmap]
rs6425282	0.88[CEU][hapmap];0.87[MEX][hapmap]
rs6425283	0.88[CEU][hapmap]
rs6425284	0.88[CEU][hapmap];0.87[MEX][hapmap]
rs6663591	0.88[AFR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6664864	0.88[CEU][hapmap];0.83[MEX][hapmap]
rs6668053	0.88[CEU][hapmap];0.87[MEX][hapmap]
rs6671824	0.88[CEU][hapmap];0.87[MEX][hapmap]
rs6672148	0.88[CEU][hapmap]
rs6683602	0.88[CEU][hapmap];0.87[MEX][hapmap]
rs6693225	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs727279	0.87[CEU][hapmap];0.87[MEX][hapmap]
rs7521870	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7523263	0.87[MEX][hapmap]
rs7523516	0.80[CHB][hapmap]
rs7538650	0.82[EUR][1000 genomes]
rs7548540	0.92[CEU][hapmap];0.91[MEX][hapmap]
rs7555533	0.88[CEU][hapmap];0.87[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 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	nsv1009056	chr1:174457532-174549665	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv999295	chr1:174457532-174596961	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
9	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
10	esv2757762	chr1:174469281-174569776	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
11	esv2758979	chr1:174469281-174569776	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
12	nsv548196	chr1:174525135-174559121	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2038025	GPR52	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174533200-174545400	Weak transcription	Primary B cells from cord blood	blood
2	chr1:174541600-174544800	Weak transcription	Primary T cells fromperipheralblood	blood

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