Variant report

Variant	rs1520575
Chromosome Location	chr3:54697592-54697593
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10510773	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs12488046	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs12490327	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12490953	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs12496821	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs12497334	0.94[MEX][hapmap];0.82[TSI][hapmap]
rs13060843	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13068008	0.90[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs13070126	0.87[ASN][1000 genomes]
rs13081682	0.94[ASN][1000 genomes]
rs13083683	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs13084347	0.88[CHD][hapmap];0.82[GIH][hapmap];0.94[MEX][hapmap];0.82[TSI][hapmap];0.86[AMR][1000 genomes]
rs13084602	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs13086256	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs13088416	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs13095178	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs13096365	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13100029	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs1344671	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs17815840	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1829549	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1882320	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1882322	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs1921548	0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs2099019	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2359861	0.86[CEU][hapmap];0.89[MEX][hapmap]
rs36021053	0.83[AMR][1000 genomes]
rs36061401	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3852006	0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs3864001	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs3868872	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs3906509	0.90[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4083342	0.80[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6798481	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6808464	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs71301895	0.88[AMR][1000 genomes]
rs72870697	0.87[ASN][1000 genomes]
rs7618235	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7623961	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs7636321	0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014595	chr3:53944473-54846754	Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv428084	chr3:54404258-54742756	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv834700	chr3:54637374-54803896	Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv525644	chr3:54653316-54709987	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1520575	ABHD6	cis	cerebellum	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54685200-54704000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:54691400-54704000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr3:54693400-54697800	Weak transcription	Right Atrium	heart
4	chr3:54693400-54702400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr3:54693600-54699200	Enhancers	Fetal Muscle Leg	muscle
6	chr3:54694000-54702200	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr3:54694000-54702400	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr3:54694000-54702600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr3:54694000-54702800	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr3:54695200-54697800	Weak transcription	Psoas Muscle	Psoas
11	chr3:54695200-54703200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr3:54695400-54697600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr3:54695400-54697600	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr3:54695400-54697800	Weak transcription	Spleen	Spleen
15	chr3:54695400-54698200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr3:54695400-54703800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr3:54695600-54697800	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr3:54695600-54702200	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr3:54695600-54704000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr3:54696400-54697600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr3:54696400-54698200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr3:54696600-54698400	Enhancers	Esophagus	oesophagus
23	chr3:54696800-54702400	Weak transcription	Fetal Stomach	stomach
24	chr3:54697000-54698400	Enhancers	NHDF-Ad	bronchial
25	chr3:54697200-54697800	Enhancers	Skeletal Muscle Male	skeletal muscle
26	chr3:54697200-54698200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr3:54697200-54699400	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr3:54697400-54699000	Enhancers	Fetal Muscle Trunk	muscle
29	chr3:54697400-54704200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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