Variant report

Variant	rs6460542
Chromosome Location	chr7:69775270-69775271
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 101 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10229027	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10229155	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10234614	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10234844	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10234892	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10235487	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10235781	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10237530	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10237685	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10244275	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10246631	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10251306	0.82[EUR][1000 genomes]
rs10251416	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10254839	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10256062	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10256186	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10258298	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10258962	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10268924	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10277411	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10280622	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1035010	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10486874	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10486875	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10499812	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10950199	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11766329	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12112638	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12155138	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12374873	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12698855	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12698866	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12698871	0.85[ASN][1000 genomes]
rs12698895	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12698896	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12698897	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12698899	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13221252	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13226923	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13228123	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1357759	0.88[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1404274	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1464786	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1464787	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1464788	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1474368	0.90[ASN][1000 genomes]
rs1524518	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1880368	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2103132	0.97[AFR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2222544	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2280613	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2280614	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2866277	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35303761	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3846984	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6460536	0.81[ASN][1000 genomes]
rs6460537	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6460541	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6460543	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6651055	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6943555	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6950647	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6953344	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6954715	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6954837	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6957740	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6961345	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6962999	0.81[ASN][1000 genomes]
rs6967697	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6967986	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6969375	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6975279	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6976581	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7781035	0.83[AMR][1000 genomes]
rs7781401	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7781727	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7784584	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7787612	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7788024	0.86[AMR][1000 genomes]
rs7790729	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7790934	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7792775	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7792964	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7796080	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7798991	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7799308	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7805470	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7808540	0.87[AMR][1000 genomes]
rs8180850	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs870920	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs873835	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9918496	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9918544	0.87[AMR][1000 genomes];0.93[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	nsv1018749	chr7:69149029-69995112	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv532782	chr7:69383651-70189959	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv916345	chr7:69520612-69784809	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv869342	chr7:69671501-69958576	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv607431	chr7:69699074-69828729	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv888337	chr7:69707076-69952187	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv529669	chr7:69709373-69974708	Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv1028870	chr7:69742438-69879231	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6460542	WBSCR17	cis	cerebellum	SCAN
rs6460542	VKORC1L1	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:69767400-69777600	Weak transcription	Primary T helper cells fromperipheralblood	blood
2	chr7:69769600-69776600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr7:69772200-69779000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
4	chr7:69773200-69777200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr7:69773400-69776400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr7:69774000-69775800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr7:69774000-69776400	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr7:69774200-69776000	Weak transcription	Primary T cells from cord blood	blood
9	chr7:69774600-69776200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr7:69775200-69776000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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