Variant report

Variant	rs10896767
Chromosome Location	chr11:58159176-58159177
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:58159136-58159207	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
OR5B15P	TF binding region

Extended variants
information (count: 76 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1047979	0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs10736689	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10792156	0.85[CHB][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap]
rs10792157	0.82[AMR][1000 genomes]
rs10792163	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10792164	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10792167	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10792172	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs10896733	0.86[ASW][hapmap];0.85[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.90[YRI][hapmap]
rs10896740	0.82[AMR][1000 genomes]
rs10896743	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10896745	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10896751	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10896752	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10896768	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10896791	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs11229332	0.82[AMR][1000 genomes]
rs11229334	0.86[AMR][1000 genomes]
rs11229337	0.85[AMR][1000 genomes]
rs11229351	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11229354	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11229356	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11229367	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11229368	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11229376	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11603523	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12794193	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12806327	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs1938648	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1938649	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1938650	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1938661	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1944050	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs1944052	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs1944054	0.90[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.85[YRI][hapmap]
rs2003230	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2186408	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2211942	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2276301	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs2507758	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs2509920	0.87[ASW][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.85[YRI][hapmap]
rs2510552	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs2510866	0.81[AFR][1000 genomes]
rs2515343	0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs2515346	0.87[ASW][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs2515347	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs2515359	0.87[ASW][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.86[YRI][hapmap]
rs2515366	0.87[ASW][hapmap];0.80[JPT][hapmap];0.97[LWK][hapmap];0.89[MKK][hapmap];0.85[YRI][hapmap]
rs4127350	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4127351	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4127352	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4255553	0.85[AMR][1000 genomes]
rs4453250	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4581466	1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4644660	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4939192	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs4939204	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6591470	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7109553	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs7112250	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7115326	0.90[CHB][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap]
rs7115653	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7117845	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs746248	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7480112	0.86[AMR][1000 genomes]
rs7926438	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7934850	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7944257	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7944352	0.87[AMR][1000 genomes]
rs7948107	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs947785	0.85[JPT][hapmap];0.85[AMR][1000 genomes]
rs956658	0.90[CHB][hapmap];0.95[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	nsv1054205	chr11:57544264-58358509	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv517849	chr11:58129053-58264181	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
3	nsv1042491	chr11:58134936-58263639	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv1037213	chr11:58142913-58178810	Enhancers ZNF genes & repeats Weak transcription	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10896767	DAK	cis	cerebellum	SCAN
rs10896767	OR8I2	cis	cerebellum	SCAN
rs10896767	OR4A16	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:58155800-58160000	Weak transcription	HSMMtube	muscle
2	chr11:58156600-58162800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr11:58158000-58159200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr11:58158200-58162800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr11:58158400-58159800	Enhancers	Placenta Amnion	Placenta Amnion
6	chr11:58158800-58162400	Enhancers	NHLF	lung
7	chr11:58159000-58162200	Enhancers	Osteobl	bone
8	chr11:58159000-58162400	Enhancers	Muscle Satellite Cultured Cells	--

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