Variant report

Variant	rs7924390
Chromosome Location	chr11:5199222-5199223
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:5191942..5195830-chr11:5198178..5202032,4	K562	blood:
2	chr11:5192167..5196032-chr11:5198178..5201494,6	K562	blood:

Variant related genes	Relation type
ENSG00000176752	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10160444	0.83[CEU][hapmap]
rs10734487	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10742552	0.90[CHB][hapmap]
rs10742559	0.84[TSI][hapmap]
rs10768638	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10768640	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10837513	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11036040	0.86[CHB][hapmap]
rs11603140	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11606639	0.93[EUR][1000 genomes]
rs11823559	0.91[EUR][1000 genomes]
rs11825768	0.92[EUR][1000 genomes]
rs4128714	0.87[CEU][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4910717	0.87[CEU][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs4910718	0.87[CEU][hapmap];0.90[EUR][1000 genomes]
rs4910719	0.89[EUR][1000 genomes]
rs4910720	0.89[EUR][1000 genomes]
rs4910722	0.90[CHB][hapmap]
rs4910724	0.82[TSI][hapmap]
rs4910726	0.87[CEU][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61880375	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6578560	0.90[CHB][hapmap]
rs6578561	0.90[CHB][hapmap]
rs6578562	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6578563	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6578567	0.90[CHB][hapmap]
rs7102118	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7114182	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7120612	0.81[MEX][hapmap];0.87[TSI][hapmap]
rs7121035	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7121172	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7131267	0.82[AMR][1000 genomes]
rs73396873	0.92[EUR][1000 genomes]
rs73396875	0.92[EUR][1000 genomes]
rs73396878	0.92[EUR][1000 genomes]
rs74051367	0.92[EUR][1000 genomes]
rs74051386	0.91[EUR][1000 genomes]
rs74051388	0.89[EUR][1000 genomes]
rs74051390	0.90[EUR][1000 genomes]
rs7479400	0.87[CEU][hapmap];0.92[EUR][1000 genomes]
rs7480442	0.87[CEU][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs7480988	0.87[CEU][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7481262	0.83[GIH][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap]
rs7481293	0.85[CEU][hapmap];0.92[EUR][1000 genomes]
rs7482238	0.89[EUR][1000 genomes]
rs7926026	0.90[EUR][1000 genomes]
rs7927539	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];0.98[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]
rs7928096	0.90[CHB][hapmap]
rs7938610	0.92[EUR][1000 genomes]
rs7938958	0.89[EUR][1000 genomes]
rs7948322	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7948470	0.89[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[MKK][hapmap];0.90[TSI][hapmap];0.81[YRI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7948698	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9804550	0.89[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:25 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054847	chr11:4642875-5200656	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
2	esv2760169	chr11:4961518-5233821	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
3	nsv553219	chr11:5026200-5214413	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
4	nsv896920	chr11:5068137-5221825	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
5	nsv896924	chr11:5098714-5221825	Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
6	nsv467668	chr11:5138733-5207389	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	27 gene(s)	inside rSNPs	diseases
7	nsv553224	chr11:5138733-5207389	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	27 gene(s)	inside rSNPs	diseases
8	nsv896925	chr11:5140977-5221825	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases
9	nsv896928	chr11:5154157-5207389	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases
10	nsv1042613	chr11:5173410-5336839	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
11	nsv1051488	chr11:5175477-5258490	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
12	nsv1048593	chr11:5183176-5261470	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
13	nsv1045187	chr11:5183176-5262622	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
14	nsv1052798	chr11:5184546-5269330	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
15	nsv1052750	chr11:5187571-5338802	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
16	nsv553225	chr11:5188827-5199222	Weak transcription Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
17	nsv1048350	chr11:5189296-5225842	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases
18	nsv896929	chr11:5192095-5271671	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
19	nsv1049387	chr11:5192334-5231273	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
20	nsv540941	chr11:5192334-5231273	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
21	nsv1038871	chr11:5192334-5301415	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
22	nsv540942	chr11:5192334-5301415	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
23	nsv1048355	chr11:5192334-5336839	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
24	nsv975828	chr11:5192464-5209037	Flanking Active TSS Enhancers Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
25	esv2752788	chr11:5193410-5226318	Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs7924390	OR52E6	cis	cerebellum	SCAN
rs7924390	OR10A5	cis	parietal	SCAN
rs7924390	CD81	cis	cerebellum	SCAN
rs7924390	OR51B6	cis	cerebellum	SCAN
rs7924390	OR52W1	cis	cerebellum	SCAN
rs7924390	OR52A1	cis	cerebellum	SCAN
rs7924390	CARS	cis	cerebellum	SCAN
rs7924390	KRTAP5-1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:5199000-5200000	Enhancers	K562	blood

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