Variant report

Variant	rs12980342
Chromosome Location	chr19:22849357-22849358
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 121 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs1125907	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11881740	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12972867	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12972909	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12973627	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12973884	0.82[EUR][1000 genomes]
rs12974328	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12974397	0.82[EUR][1000 genomes]
rs12978511	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12978794	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.82[EUR][1000 genomes]
rs12978964	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12979173	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12979848	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12983260	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12983761	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12984634	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12984903	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1433085	0.82[EUR][1000 genomes]
rs16999519	0.82[EUR][1000 genomes]
rs16999554	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1835993	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1835994	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1864004	0.81[CEU][hapmap];0.94[GIH][hapmap];0.82[MEX][hapmap]
rs1897602	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1963578	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1963579	0.83[EUR][1000 genomes]
rs1984783	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2082445	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2099341	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2361021	0.82[EUR][1000 genomes]
rs2361022	0.82[EUR][1000 genomes]
rs2361023	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.82[EUR][1000 genomes]
rs2361245	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2885221	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2885222	0.83[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs34563787	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34682021	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34839858	0.82[EUR][1000 genomes]
rs35007247	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35023140	0.83[ASN][1000 genomes]
rs35085463	0.82[EUR][1000 genomes]
rs35355374	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35731237	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35740274	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3745116	0.85[AFR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3951783	0.81[ASN][1000 genomes]
rs4414616	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4627499	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4932782	0.82[EUR][1000 genomes]
rs4933017	0.82[EUR][1000 genomes]
rs4933019	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4933020	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4933021	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4933031	0.81[CEU][hapmap];0.94[GIH][hapmap];0.82[MEX][hapmap]
rs4933032	0.81[CEU][hapmap];0.94[GIH][hapmap];0.82[MEX][hapmap]
rs56247961	0.83[AFR][1000 genomes]
rs56271774	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56271778	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56663398	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56968124	0.82[EUR][1000 genomes]
rs57775631	0.82[EUR][1000 genomes]
rs58037286	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58265266	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58998018	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60675447	0.82[EUR][1000 genomes]
rs62118818	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62118819	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62118823	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62118824	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62118829	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62118830	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6511367	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs66620859	0.84[AFR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs71355986	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7245634	0.81[CEU][hapmap]
rs7246908	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7246932	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7248841	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7248993	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7249001	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7250111	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7250285	0.85[AFR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7250343	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7251887	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73018802	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73020703	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73028776	0.82[EUR][1000 genomes]
rs73028793	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7409004	0.84[AFR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7507680	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7507688	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7507785	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8102469	0.81[CEU][hapmap];0.94[GIH][hapmap];0.82[MEX][hapmap]
rs8105596	0.80[CEU][hapmap]
rs8106204	0.82[YRI][hapmap]
rs919780	0.82[EUR][1000 genomes]
rs937078	0.82[EUR][1000 genomes]
rs9710074	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3360126	chr19:22209871-23199213	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
2	esv3333410	chr19:22213338-23199725	ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
3	nsv525240	chr19:22250912-23216667	ZNF genes & repeats Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
4	esv3363663	chr19:22320301-23103053	Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
5	nsv911440	chr19:22325391-23216667	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
6	nsv819194	chr19:22336264-23223696	ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
7	nsv911443	chr19:22338142-22899585	Active TSS ZNF genes & repeats Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
8	nsv911444	chr19:22338142-23198437	ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
9	nsv911445	chr19:22346403-22899585	Weak transcription Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
10	nsv819205	chr19:22346403-23199700	Weak transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
11	nsv1064071	chr19:22359491-23153773	Weak transcription ZNF genes & repeats Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
12	nsv543957	chr19:22359491-23153773	Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
13	nsv932157	chr19:22359492-23192975	Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
14	esv3387241	chr19:22383621-23175441	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
15	nsv1059925	chr19:22408435-23083293	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
16	nsv1056393	chr19:22408435-23106126	Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
17	esv3496801	chr19:22635989-23028182	Enhancers ZNF genes & repeats Active TSS Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
18	esv3496802	chr19:22635989-23028182	Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
19	esv3529242	chr19:22650256-22863256	Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
20	esv3529243	chr19:22650256-22863256	Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
21	nsv1062447	chr19:22818831-22879285	Weak transcription ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases
22	nsv911451	chr19:22826728-23198437	Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
23	nsv9684	chr19:22848155-22854467	ZNF genes & repeats Weak transcription	lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12980342	ZNF492	Cis_1M	lymphoblastoid	RTeQTL
rs12980342	CILP2	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:22848200-22849400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr19:22849000-22849400	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
3	chr19:22849000-22849600	ZNF genes & repeats	Dnd41	blood

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