Variant report

Variant	rs6656747
Chromosome Location	chr1:63230135-63230136
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 92 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10159426	0.92[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.89[MEX][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10493327	0.88[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10736399	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10749734	0.86[ASN][1000 genomes]
rs10789124	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10789125	0.90[ASN][1000 genomes]
rs10789129	0.89[ASN][1000 genomes]
rs10889366	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10889371	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10889372	0.92[ASN][1000 genomes]
rs10889374	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10889375	0.91[ASN][1000 genomes]
rs10889376	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10889383	0.92[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.86[ASN][1000 genomes]
rs10889384	0.86[ASN][1000 genomes]
rs10889386	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11208013	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11208019	0.91[ASN][1000 genomes]
rs11208021	0.80[ASN][1000 genomes]
rs11208023	0.92[ASN][1000 genomes]
rs11208024	0.92[ASN][1000 genomes]
rs11208025	0.93[ASN][1000 genomes]
rs11208026	0.93[ASN][1000 genomes]
rs11208027	0.91[ASN][1000 genomes]
rs11208032	0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11208035	0.89[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11208037	0.89[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11208038	0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11208040	0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11208043	0.80[ASN][1000 genomes]
rs11208045	0.81[ASN][1000 genomes]
rs11208046	0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11208047	0.90[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11579171	0.88[ASN][1000 genomes]
rs11579518	0.84[ASN][1000 genomes]
rs11587081	1.00[JPT][hapmap]
rs11807368	0.93[ASN][1000 genomes]
rs12085904	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12120847	0.83[ASN][1000 genomes]
rs12129919	0.88[ASN][1000 genomes]
rs12134455	0.82[ASN][1000 genomes]
rs12138091	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12567340	0.88[ASN][1000 genomes]
rs12567999	0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12752360	0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1333733	0.92[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.82[ASN][1000 genomes]
rs1333736	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs1360677	0.92[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs1413242	0.82[ASN][1000 genomes]
rs1981067	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs2149115	0.86[ASN][1000 genomes]
rs2366820	0.83[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2366821	0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2366822	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2803238	0.82[GIH][hapmap]
rs2886770	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2886771	0.81[ASN][1000 genomes]
rs3211074	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs3737893	0.89[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4396149	0.93[ASN][1000 genomes]
rs4448545	1.00[JPT][hapmap]
rs6587990	0.89[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6587991	0.82[ASN][1000 genomes]
rs6657707	0.88[ASN][1000 genomes]
rs6660873	0.84[ASN][1000 genomes]
rs6663165	0.95[CEU][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6664372	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6664673	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6664677	0.92[ASN][1000 genomes]
rs6665455	0.88[ASN][1000 genomes]
rs6670694	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs6676637	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs6679582	0.88[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.86[ASN][1000 genomes]
rs6682286	0.81[ASN][1000 genomes]
rs6683423	0.92[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.88[ASN][1000 genomes]
rs6683832	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6686232	0.89[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6687943	0.92[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6695607	0.81[ASN][1000 genomes]
rs6699457	0.88[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6702274	0.90[ASN][1000 genomes]
rs7414021	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7512374	0.81[ASN][1000 genomes]
rs7512529	0.81[ASN][1000 genomes]
rs7517722	0.86[ASN][1000 genomes]
rs7519205	0.85[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7521483	1.00[JPT][hapmap]
rs7524508	0.81[ASN][1000 genomes]
rs7531329	0.84[ASN][1000 genomes]
rs7540030	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.80[MEX][hapmap];0.82[MKK][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7543380	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7546804	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6656747	ATG4C	cis	Thyroid	GTEx
rs6656747	ATG4C///CTR9	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:63225800-63231400	Weak transcription	Right Atrium	heart
2	chr1:63227000-63231600	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr1:63227200-63231400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr1:63227200-63231600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr1:63227800-63231800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr1:63228200-63231400	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr1:63228600-63231800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:63228800-63234200	Weak transcription	Placenta	Placenta

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