Variant report

Variant	rs499397
Chromosome Location	chr1:57766056-57766057
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:57762959..57764733-chr1:57765610..57768208,2	K562	blood:

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1149628	0.96[CEU][hapmap];0.95[CHB][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1424473	1.00[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs197626	1.00[CHB][hapmap];0.82[CHD][hapmap];0.84[JPT][hapmap]
rs197638	1.00[CHB][hapmap];0.82[CHD][hapmap];0.84[JPT][hapmap]
rs197644	1.00[CHB][hapmap];0.84[CHD][hapmap];0.84[JPT][hapmap]
rs1991093	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2251472	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs2432690	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2656093	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2656094	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2764664	0.81[MEX][hapmap]
rs2764665	0.91[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs485723	0.84[EUR][1000 genomes]
rs486809	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs487566	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs492781	0.85[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.87[ASN][1000 genomes]
rs501921	0.85[EUR][1000 genomes]
rs508389	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs511707	0.81[MEX][hapmap]
rs542873	1.00[CHB][hapmap];0.81[CHD][hapmap];0.84[JPT][hapmap]
rs542949	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs545582	0.81[MEX][hapmap]
rs545671	0.93[EUR][1000 genomes]
rs568843	0.86[EUR][1000 genomes]
rs572092	1.00[CHB][hapmap]
rs576038	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs581886	0.81[MEX][hapmap]
rs584147	1.00[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs587046	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs595513	0.89[CEU][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs595568	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs596784	0.81[MEX][hapmap]
rs597941	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs610360	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs611276	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs611606	0.88[CEU][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs614488	1.00[CHB][hapmap];0.82[CHD][hapmap];0.84[JPT][hapmap]
rs620214	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs622423	0.81[MEX][hapmap]
rs627489	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs627550	1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs627936	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs634391	0.81[CEU][hapmap];0.86[MEX][hapmap];0.81[AMR][1000 genomes]
rs642526	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs643382	0.89[CEU][hapmap];0.83[GIH][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs648607	0.81[MEX][hapmap]
rs657612	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs659069	0.86[CHB][hapmap]
rs663975	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs674966	0.81[MEX][hapmap]
rs675075	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs680197	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs706385	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]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs499397	C1orf177	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57747600-57769400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr1:57751600-57770600	Weak transcription	Fetal Intestine Large	intestine
3	chr1:57763600-57768000	Weak transcription	Fetal Brain Female	brain
4	chr1:57763600-57769000	Weak transcription	Fetal Brain Male	brain
5	chr1:57765600-57766400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:57765600-57766400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:57765600-57767800	Strong transcription	Fetal Intestine Small	intestine
8	chr1:57766000-57766200	Enhancers	H9 Cell Line	embryonic stem cell
9	chr1:57766000-57767200	Weak transcription	HUES64 Cell Line	embryonic stem cell

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