Variant report

Variant	rs856119
Chromosome Location	chr1:158899747-158899748
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 77 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs1102018	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2260107	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2427820	0.80[EUR][1000 genomes]
rs2427822	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs2494075	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2511204	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs2518515	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs2518517	0.80[EUR][1000 genomes]
rs2518519	0.80[EUR][1000 genomes]
rs2518534	0.80[EUR][1000 genomes]
rs2518543	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2518544	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2518545	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2518546	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2518547	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2518548	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];0.80[EUR][1000 genomes]
rs2518549	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs2518550	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs2518551	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs2518552	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs2793850	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2793852	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2793853	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2793854	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2820126	0.82[EUR][1000 genomes]
rs2820147	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs2820148	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs2820149	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs2820150	0.94[CEU][hapmap];1.00[JPT][hapmap]
rs2820151	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs2820152	0.92[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs2820153	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];0.80[EUR][1000 genomes]
rs2820156	0.80[EUR][1000 genomes]
rs2820157	0.80[EUR][1000 genomes]
rs2820162	0.80[EUR][1000 genomes]
rs2820167	0.80[EUR][1000 genomes]
rs2820191	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2820192	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2820194	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2820195	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2852652	0.80[EUR][1000 genomes]
rs2852656	1.00[JPT][hapmap]
rs2852662	0.80[EUR][1000 genomes]
rs2852663	0.80[EUR][1000 genomes]
rs2852664	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs2852666	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs2852667	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs2852687	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2852688	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2852703	0.80[EUR][1000 genomes]
rs2852704	0.80[EUR][1000 genomes]
rs2852710	0.94[CEU][hapmap];1.00[JPT][hapmap]
rs2852711	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs2852712	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs4338350	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs7419186	0.80[EUR][1000 genomes]
rs856096	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs856103	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs856104	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs856105	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs856107	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs856108	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs856109	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs856112	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs856114	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs856115	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs856116	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs856117	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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs856118	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs856123	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs856151	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs860636	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002401	chr1:158712627-158972031	Flanking Active TSS Strong transcription Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	esv3376764	chr1:158761947-158998617	Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv872484	chr1:158863845-158909164	Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv872485	chr1:158863845-158922287	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv1007597	chr1:158874806-158934301	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs856119	ASH1L	cis	cerebellum	SCAN
rs856119	KCNN3	cis	parietal	SCAN
rs856119	LY9	cis	parietal	SCAN
rs856119	BGLAP	cis	cerebellum	SCAN
rs856119	SLAMF1	cis	cerebellum	SCAN
rs856119	EFNA1	cis	cerebellum	SCAN
rs856119	CREB3L4	cis	cerebellum	SCAN
rs856119	GPATCH4	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:158898200-158900200	Enhancers	Primary T killer memory cells from peripheral blood	blood
2	chr1:158898600-158900400	Enhancers	Primary T cells fromperipheralblood	blood
3	chr1:158898800-158899800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr1:158899000-158900200	Enhancers	Primary T helper naive cells from peripheral blood	blood
5	chr1:158899000-158900200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr1:158899200-158899800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
7	chr1:158899200-158900000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr1:158899200-158900600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr1:158899400-158900400	Enhancers	Primary T cells from cord blood	blood
10	chr1:158899600-158900000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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