Variant report

Variant	rs394487
Chromosome Location	chr6:160778639-160778640
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 88 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1018234	0.82[CEU][hapmap];0.81[JPT][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1510225	0.82[CEU][hapmap];0.80[JPT][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes]
rs1510229	0.82[CEU][hapmap];0.81[JPT][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes]
rs1567438	0.86[CEU][hapmap]
rs1567442	0.82[CEU][hapmap]
rs1605965	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2063345	0.87[CEU][hapmap];0.80[EUR][1000 genomes]
rs2174914	0.87[CEU][hapmap];0.80[EUR][1000 genomes]
rs2175251	0.88[EUR][1000 genomes]
rs2457575	0.87[CEU][hapmap];0.80[EUR][1000 genomes]
rs2457576	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs2504937	0.86[CEU][hapmap];0.86[EUR][1000 genomes]
rs2661834	0.86[CEU][hapmap]
rs2661845	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2665358	0.83[EUR][1000 genomes]
rs316172	0.83[ASN][1000 genomes]
rs316177	0.82[ASN][1000 genomes]
rs316244	0.82[CEU][hapmap];0.81[JPT][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes]
rs366608	0.82[ASN][1000 genomes]
rs367213	0.81[ASN][1000 genomes]
rs372665	0.83[ASN][1000 genomes]
rs377551	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs383420	0.81[ASN][1000 genomes]
rs394352	0.81[JPT][hapmap];0.83[TSI][hapmap];0.87[EUR][1000 genomes]
rs394468	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap]
rs396843	0.81[ASN][1000 genomes]
rs401746	0.80[ASN][1000 genomes]
rs402219	0.82[CEU][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs405405	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs416879	0.94[ASN][1000 genomes]
rs420038	0.82[CEU][hapmap];0.81[JPT][hapmap];0.83[TSI][hapmap];0.87[EUR][1000 genomes]
rs423961	0.83[ASN][1000 genomes]
rs425983	0.83[ASN][1000 genomes]
rs431747	0.82[ASN][1000 genomes]
rs435421	0.82[ASN][1000 genomes]
rs440962	0.82[CEU][hapmap];0.81[JPT][hapmap];0.83[TSI][hapmap];0.87[EUR][1000 genomes]
rs443043	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs445849	0.82[ASN][1000 genomes]
rs446926	0.82[CEU][hapmap];0.81[JPT][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs474513	0.95[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.85[MKK][hapmap];0.93[ASN][1000 genomes]
rs486339	0.94[ASN][1000 genomes]
rs486359	0.80[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs487060	0.95[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs487152	0.95[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.85[MKK][hapmap];0.94[ASN][1000 genomes]
rs490275	0.82[ASN][1000 genomes]
rs501470	0.95[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.85[MKK][hapmap];0.93[ASN][1000 genomes]
rs505870	0.95[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.85[MKK][hapmap];0.93[ASN][1000 genomes]
rs506823	0.93[ASN][1000 genomes]
rs509707	0.94[ASN][1000 genomes]
rs518295	0.95[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.85[MKK][hapmap];0.94[ASN][1000 genomes]
rs519118	0.95[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];0.89[MKK][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs520685	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs520829	0.83[ASN][1000 genomes]
rs537937	0.82[ASN][1000 genomes]
rs539298	0.95[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.83[MKK][hapmap];0.93[ASN][1000 genomes]
rs539958	0.95[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.85[MKK][hapmap];0.94[ASN][1000 genomes]
rs541091	0.91[ASN][1000 genomes]
rs543159	0.93[ASN][1000 genomes]
rs547290	0.83[ASN][1000 genomes]
rs555754	0.92[ASN][1000 genomes]
rs569919	0.91[CEU][hapmap];0.89[CHD][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.83[ASN][1000 genomes]
rs575796	0.86[CHD][hapmap];0.83[ASN][1000 genomes]
rs581556	0.94[ASN][1000 genomes]
rs609562	0.94[ASN][1000 genomes]
rs622217	0.89[CHD][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs624319	0.95[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs634916	0.81[ASN][1000 genomes]
rs637614	0.94[ASN][1000 genomes]
rs639426	0.94[ASN][1000 genomes]
rs641990	0.95[JPT][hapmap]
rs668871	0.92[ASN][1000 genomes]
rs673259	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs675162	0.80[GIH][hapmap];0.90[JPT][hapmap]
rs695174	0.94[ASN][1000 genomes]
rs9346816	0.95[JPT][hapmap]
rs9364552	0.95[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758089	chr6:160372244-161234665	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	esv2759484	chr6:160372244-161234665	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	esv35098	chr6:160422589-161070870	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	esv2757197	chr6:160432331-161070870	Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv818463	chr6:160435569-161025547	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv1030746	chr6:160592321-160867031	Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv538493	chr6:160592321-160867031	Weak transcription Bivalent/Poised TSS Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1030171	chr6:160648469-161091864	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
9	nsv886809	chr6:160670494-160979275	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
10	nsv886810	chr6:160700769-160897872	Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
11	nsv886811	chr6:160700769-161070990	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
12	nsv886812	chr6:160706661-161024848	Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs394487	C19orf54	trans	cerebellum	SCAN
rs394487	GLI4	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:160771200-160780400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:160773400-160779400	Weak transcription	Ovary	ovary
3	chr6:160774200-160783000	Weak transcription	Stomach Smooth Muscle	stomach
4	chr6:160774400-160779200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr6:160774400-160780000	Enhancers	Skeletal Muscle Female	skeletal muscle
6	chr6:160775400-160790800	Weak transcription	Right Atrium	heart
7	chr6:160775800-160778800	Enhancers	Fetal Muscle Trunk	muscle
8	chr6:160776200-160779200	Weak transcription	Adipose Nuclei	Adipose
9	chr6:160776200-160779800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr6:160776200-160780200	Enhancers	A549	lung
11	chr6:160776400-160779600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr6:160776400-160781600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr6:160776400-160781600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr6:160776400-160781600	Weak transcription	HMEC	breast
15	chr6:160776400-160781600	Weak transcription	NHEK	skin
16	chr6:160776400-160781800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr6:160776400-160783600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr6:160776400-160786000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr6:160776800-160780000	Enhancers	Fetal Muscle Leg	muscle
20	chr6:160777000-160779200	Weak transcription	Placenta	Placenta
21	chr6:160777600-160778800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr6:160778200-160784400	Weak transcription	Lung	lung
23	chr6:160778400-160779000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr6:160778400-160779200	Weak transcription	Aorta	Aorta
25	chr6:160778400-160779400	Weak transcription	Liver	Liver
26	chr6:160778400-160779400	Weak transcription	Psoas Muscle	Psoas
27	chr6:160778400-160791000	Weak transcription	Gastric	stomach
28	chr6:160778600-160779200	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr6:160778600-160780400	Enhancers	HepG2	liver

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