Variant report

Variant	rs7535496
Chromosome Location	chr1:63348556-63348557
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 101 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10159426	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10493327	0.89[JPT][hapmap]
rs10736399	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10789129	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10889383	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10889384	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10889385	0.81[ASN][1000 genomes]
rs10889386	1.00[CEU][hapmap];0.83[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10889387	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11208032	0.90[JPT][hapmap]
rs11208035	0.89[JPT][hapmap]
rs11208037	0.89[JPT][hapmap]
rs11208038	0.90[JPT][hapmap]
rs11208040	0.89[JPT][hapmap]
rs11208043	0.80[ASN][1000 genomes]
rs11208046	0.89[JPT][hapmap]
rs11208047	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11208049	0.88[ASN][1000 genomes]
rs11208050	0.85[ASN][1000 genomes]
rs11208051	0.88[ASN][1000 genomes]
rs11208052	0.89[ASN][1000 genomes]
rs11208056	0.92[ASN][1000 genomes]
rs11580642	0.93[ASN][1000 genomes]
rs11584363	0.85[ASN][1000 genomes]
rs11587081	0.84[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs11803404	0.86[ASN][1000 genomes]
rs11804568	0.92[ASN][1000 genomes]
rs12128286	0.86[ASN][1000 genomes]
rs12567999	0.90[JPT][hapmap]
rs12725996	0.89[ASN][1000 genomes]
rs12728111	0.93[ASN][1000 genomes]
rs12742537	0.93[ASN][1000 genomes]
rs12743698	0.82[ASN][1000 genomes]
rs12748640	0.82[ASN][1000 genomes]
rs12749904	0.89[ASN][1000 genomes]
rs12752360	0.90[JPT][hapmap]
rs12756081	0.89[ASN][1000 genomes]
rs1333730	0.88[ASN][1000 genomes]
rs1333733	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1333734	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1333736	0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs1360677	1.00[CEU][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1360678	0.84[ASN][1000 genomes]
rs1413242	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1537496	0.89[ASN][1000 genomes]
rs17097064	0.86[ASN][1000 genomes]
rs1931079	0.85[ASN][1000 genomes]
rs1981067	0.85[CHB][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs2050248	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2366820	0.89[JPT][hapmap]
rs2366821	0.90[JPT][hapmap]
rs2366822	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2803238	0.89[CHB][hapmap]
rs2886770	1.00[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3211074	0.84[CHB][hapmap];0.89[JPT][hapmap]
rs3737892	0.81[ASN][1000 genomes]
rs3737893	0.89[JPT][hapmap]
rs4448545	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs6587990	0.89[JPT][hapmap]
rs6587992	0.82[ASN][1000 genomes]
rs6587993	0.82[ASN][1000 genomes]
rs6587994	0.82[ASN][1000 genomes]
rs6587996	0.86[ASN][1000 genomes]
rs6587997	0.89[ASN][1000 genomes]
rs6587998	0.89[ASN][1000 genomes]
rs6656119	0.86[ASN][1000 genomes]
rs6657552	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6663165	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6664673	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6665455	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6670072	0.85[ASN][1000 genomes]
rs6670694	0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs6676637	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs6676821	0.84[ASN][1000 genomes]
rs6677051	0.82[ASN][1000 genomes]
rs6679582	0.96[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6683423	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6683732	0.84[ASN][1000 genomes]
rs6683832	1.00[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];0.95[YRI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6685784	0.89[ASN][1000 genomes]
rs6686232	0.89[JPT][hapmap]
rs6687943	1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6693530	0.89[ASN][1000 genomes]
rs6699457	0.96[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7414021	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7512480	0.83[CHB][hapmap]
rs7515960	0.89[ASN][1000 genomes]
rs7519205	0.85[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs7521483	0.85[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs7522726	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7526246	0.93[ASN][1000 genomes]
rs7527423	0.86[ASN][1000 genomes]
rs7527905	0.82[ASN][1000 genomes]
rs7531329	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7540030	1.00[CEU][hapmap];0.83[CHB][hapmap];0.89[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7540205	0.84[ASN][1000 genomes]
rs7543380	0.85[EUR][1000 genomes]
rs7553110	0.85[ASN][1000 genomes]
rs7555606	0.85[ASN][1000 genomes]
rs998096	0.86[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830015	chr1:63261143-63455296	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7535496	ATG4C	cis	Thyroid	GTEx
rs7535496	ATG4C///CTR9	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:63346800-63349600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr1:63346800-63349600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:63347000-63349000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr1:63347000-63349600	Enhancers	Brain Germinal Matrix	brain
5	chr1:63347400-63348800	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr1:63347600-63348600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr1:63347600-63348600	Enhancers	HepG2	liver
8	chr1:63347800-63348600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:63348000-63348600	Enhancers	H9 Cell Line	embryonic stem cell
10	chr1:63348000-63348600	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr1:63348000-63348600	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr1:63348000-63348600	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr1:63348000-63348800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr1:63348000-63348800	Enhancers	Fetal Brain Male	brain
15	chr1:63348000-63350600	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr1:63348200-63348600	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr1:63348400-63349400	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr1:63348400-63349400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr1:63348400-63349600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr1:63348400-63353000	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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