Variant report

Variant	rs316005
Chromosome Location	chr6:160646280-160646281
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs2448295	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2450975	0.81[CEU][hapmap];0.97[GIH][hapmap];0.83[EUR][1000 genomes]
rs2619264	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2619270	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2634654	0.83[EUR][1000 genomes]
rs2774218	0.83[EUR][1000 genomes]
rs2774230	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2774232	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2928034	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2928036	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs315979	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs315980	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs315981	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs315982	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs315983	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs315984	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs315985	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs315987	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs315988	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs315989	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs315990	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs315993	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs315994	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs315995	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs315999	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs316000	0.80[CEU][hapmap];0.97[GIH][hapmap];0.82[EUR][1000 genomes]
rs316001	0.83[EUR][1000 genomes]
rs316003	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316004	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316006	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316007	0.82[CEU][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs316008	0.82[CEU][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs316011	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs316012	0.88[CEU][hapmap];0.81[CHB][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.92[EUR][1000 genomes]
rs316013	0.82[CEU][hapmap];0.81[CHB][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs316014	0.82[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs316015	0.88[CEU][hapmap];0.81[CHB][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs316016	0.82[CEU][hapmap];0.81[CHB][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs316017	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs316018	0.82[CEU][hapmap];0.81[CHB][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.92[EUR][1000 genomes]
rs316021	0.88[CEU][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs316022	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34360089	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3798160	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs479078	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs515140	0.94[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs543435	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs582158	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs595374	0.83[EUR][1000 genomes]
rs610206	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs617217	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs625438	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs638360	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs657051	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9457875	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9457878	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv886808	chr6:160625978-160652929	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs316005	QKI	cis	cerebellum	SCAN
rs316005	MAS1	cis	cerebellum	SCAN
rs316005	RSPH3	cis	cerebellum	SCAN
rs316005	WTAP	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:160640400-160651200	Weak transcription	Stomach Smooth Muscle	stomach
2	chr6:160643200-160646400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr6:160643800-160647000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr6:160643800-160647000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr6:160643800-160648400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr6:160644000-160668600	Weak transcription	Aorta	Aorta
7	chr6:160644200-160646600	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr6:160644400-160646400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr6:160644400-160646800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr6:160645000-160649000	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr6:160645200-160647000	Weak transcription	Esophagus	oesophagus
12	chr6:160645600-160649400	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr6:160645800-160649600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr6:160646000-160647600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr6:160646000-160648800	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr6:160646000-160648800	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr6:160646000-160649000	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr6:160646200-160649200	Enhancers	iPS-15b Cell Line	embryonic stem cell

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