Variant report

Variant	rs706385
Chromosome Location	chr1:57749903-57749904
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 76 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1149628	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1424473	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1910690	0.88[ASN][1000 genomes]
rs197625	0.86[ASN][1000 genomes]
rs197626	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs197638	1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs197644	1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs197645	0.86[ASN][1000 genomes]
rs197649	0.88[ASN][1000 genomes]
rs1991093	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2251472	1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs2432690	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs2656093	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2656094	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2656095	0.81[JPT][hapmap];0.80[MEX][hapmap]
rs2764664	0.90[MEX][hapmap]
rs2764665	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.83[TSI][hapmap];0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs485723	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs486809	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs487566	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs488405	0.88[ASN][1000 genomes]
rs492781	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs492905	0.88[ASN][1000 genomes]
rs493846	0.88[ASN][1000 genomes]
rs499397	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.83[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs501921	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs508389	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs511707	0.81[JPT][hapmap];0.90[MEX][hapmap]
rs515802	0.88[ASN][1000 genomes]
rs529527	0.86[ASN][1000 genomes]
rs537441	0.81[ASN][1000 genomes]
rs539229	0.85[ASN][1000 genomes]
rs542873	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs542949	1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs545582	0.90[MEX][hapmap];0.81[TSI][hapmap]
rs545671	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs561531	0.81[JPT][hapmap]
rs568843	0.93[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs572092	1.00[CHB][hapmap];0.93[CHD][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs576038	0.84[EUR][1000 genomes]
rs581886	0.90[MEX][hapmap];0.81[TSI][hapmap];0.80[EUR][1000 genomes]
rs584147	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.83[TSI][hapmap];0.91[ASN][1000 genomes]
rs587046	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs593154	0.88[ASN][1000 genomes]
rs595513	0.92[CEU][hapmap];0.93[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs595568	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs596784	0.90[MEX][hapmap];0.83[TSI][hapmap]
rs597941	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs610360	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs611276	1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs611606	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs614488	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs620214	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs622423	0.90[MEX][hapmap];0.81[TSI][hapmap];0.80[EUR][1000 genomes]
rs627489	1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs627550	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs627936	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs634391	0.85[CEU][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs637379	0.80[EUR][1000 genomes]
rs642526	0.92[CEU][hapmap];0.81[JPT][hapmap];0.84[EUR][1000 genomes]
rs643382	1.00[ASW][hapmap];0.92[CEU][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs648607	0.81[LWK][hapmap];0.90[MEX][hapmap];0.90[MKK][hapmap];0.89[TSI][hapmap]
rs655277	0.88[ASN][1000 genomes]
rs657612	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs659069	0.86[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs663975	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66894620	0.84[ASN][1000 genomes]
rs669931	0.85[ASN][1000 genomes]
rs674966	0.81[LWK][hapmap];0.90[MEX][hapmap];0.90[MKK][hapmap];0.89[TSI][hapmap]
rs675075	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs680197	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs686702	0.88[ASN][1000 genomes]
rs693942	0.86[ASN][1000 genomes]
rs833626	0.80[EUR][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	nsv461628	chr1:57463326-57816489	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv546305	chr1:57463326-57816489	Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs706385	C1orf177	cis	parietal	SCAN
rs706385	ACOT11	cis	parietal	SCAN
rs706385	C1orf175	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57742200-57755400	Weak transcription	Fetal Brain Male	brain
2	chr1:57744600-57751200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:57747600-57769400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr1:57748400-57755200	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr1:57749200-57750600	Weak transcription	Liver	Liver
6	chr1:57749400-57751000	Weak transcription	Fetal Intestine Small	intestine
7	chr1:57749600-57751200	Weak transcription	Fetal Intestine Large	intestine

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