Variant report

Variant	rs12611334
Chromosome Location	chr19:40229409-40229410
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr19:40229390-40229979	HL-60	blood:	n/a	n/a
2	SPI1	chr19:40229404-40229916	GM12891	blood:	n/a	n/a
3	SPI1	chr19:40229325-40230094	GM12878	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:40229366-40229416	AG10803	skin:	n/a
2	chr19:40229366-40229416	HMEC	breast:	n/a
3	chr19:40229366-40229416	HAEpiC	amniotic membrane:	n/a
4	chr19:40229366-40229416	SK-N-MC	brain:	n/a
5	chr19:40229366-40229416	PrEC	prostate:	n/a
6	chr19:40229366-40229416	GM19239	blood:	n/a
7	chr19:40229366-40229416	AG09309	skin:	n/a
8	chr19:40229366-40229416	SKMC	muscle:	n/a
9	chr19:40229366-40229416	GM12878	blood:	n/a
10	chr19:40229366-40229416	HCM	heart:	n/a
11	chr19:40229366-40229416	K562	blood:	n/a
12	chr19:40229366-40229416	GM06990	blood:	n/a
13	chr19:40229366-40229416	SK-N-SH_RA	brain:	n/a
14	chr19:40229366-40229416	RPTEC	kidney:	n/a
15	chr19:40229366-40229416	ovcar-3	ovarian:	n/a
16	chr19:40229366-40229416	LNCaP	prostate:	n/a
17	chr19:40229366-40229416	T-47D	breast:	n/a
18	chr19:40229366-40229416	HPAEpiC	pulmonary alveolar:	n/a
19	chr19:40229366-40229416	Hepatocyte	liver:	n/a
20	chr19:40229366-40229416	SAEC	small airway:	n/a
21	chr19:40229366-40229416	H1-hESC	embryonic stem cell:	embryo
22	chr19:40229366-40229416	HCPEpiC	choroid plexus:	n/a
23	chr19:40229366-40229416	BJ	skin:	n/a
24	chr19:40229366-40229416	BE2_C	brain:	n/a
25	chr19:40229366-40229416	HIPEpiC	eye:	n/a
26	chr19:40229366-40229416	NHDF-neo	bronchial:	n/a
27	chr19:40229366-40229416	HNPCEpiC	eye:	n/a
28	chr19:40229366-40229416	MCF10A-Er-Src	breast:	n/a
29	chr19:40229366-40229416	CMK	blood:	n/a
30	chr19:40229366-40229416	ProgFib	skin:	n/a
31	chr19:40229366-40229416	NB4	blood:	n/a
32	chr19:40229366-40229416	AG04450	lung:	fetal
33	chr19:40229366-40229416	Jurkat	blood:	n/a
34	chr19:40229366-40229416	HEEpiC	esophagus:	n/a
35	chr19:40229366-40229416	HEK293	kidney:	embryo
36	chr19:40229366-40229416	Caco-2	colon:	n/a
37	chr19:40229366-40229416	SK-N-SH	brain:	n/a
38	chr19:40229366-40229416	NH-A	brain:	n/a
39	chr19:40229366-40229416	GM12891	blood:	n/a
40	chr19:40229366-40229416	Hela-S3	cervix:	n/a
41	chr19:40229366-40229416	HCT-116	colon:	n/a
42	chr19:40229366-40229416	AG04449	skin:	fetal
43	chr19:40229366-40229416	HL-60	blood:	n/a
44	chr19:40229366-40229416	U87	brain:	n/a
45	chr19:40229366-40229416	HRCEpiC	kidney:	n/a
46	chr19:40229366-40229416	MCF-7	breast:	n/a
47	chr19:40229366-40229416	HRPEpiC	eye:	n/a
48	chr19:40229366-40229416	PFSK-1	brain:	n/a
49	chr19:40229366-40229416	IMR90	lung:	fetal
50	chr19:40229366-40229416	GM12892	blood:	n/a

No data

Variant related genes	Relation type
CLC	TF binding region
CLC	CpG island

Extended variants
information (count: 95 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10421474	1.00[ASN][1000 genomes]
rs11083534	0.83[EUR][1000 genomes]
rs11083535	0.94[ASN][1000 genomes]
rs11666142	0.94[ASN][1000 genomes]
rs11666190	0.94[ASN][1000 genomes]
rs11666517	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11669501	0.94[ASN][1000 genomes]
rs11669658	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11670568	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11878990	0.93[ASN][1000 genomes]
rs11879130	0.93[ASN][1000 genomes]
rs11881937	0.87[ASN][1000 genomes]
rs11883181	0.94[ASN][1000 genomes]
rs12609196	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12610197	0.94[ASN][1000 genomes]
rs12610386	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12610398	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12610904	0.94[ASN][1000 genomes]
rs12610934	0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12611052	0.93[ASN][1000 genomes]
rs12611097	0.93[ASN][1000 genomes]
rs16973570	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17641958	0.88[CEU][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17709242	0.96[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1985359	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286757	0.96[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2355335	1.00[CHB][hapmap];0.96[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs28816119	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35332571	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3810387	0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs3810388	0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs3810389	0.92[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.85[MKK][hapmap];0.87[ASN][1000 genomes]
rs3810392	0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs3810396	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3826923	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs386545	0.97[ASN][1000 genomes]
rs3922304	0.96[CEU][hapmap];0.83[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4141230	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4141231	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4629090	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55678764	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55850506	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56205202	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56243473	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56261485	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56346568	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56400901	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57145045	0.87[ASN][1000 genomes]
rs58920360	0.87[ASN][1000 genomes]
rs59097080	0.94[ASN][1000 genomes]
rs60928622	0.87[ASN][1000 genomes]
rs61208282	0.93[ASN][1000 genomes]
rs62121666	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62121667	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62121738	0.95[ASN][1000 genomes]
rs62121739	0.93[ASN][1000 genomes]
rs62121741	0.94[ASN][1000 genomes]
rs62121742	0.94[ASN][1000 genomes]
rs62121748	0.93[ASN][1000 genomes]
rs62121749	0.93[ASN][1000 genomes]
rs62121750	0.88[ASN][1000 genomes]
rs62121753	0.87[ASN][1000 genomes]
rs62121754	0.87[ASN][1000 genomes]
rs62121755	0.87[ASN][1000 genomes]
rs62121756	0.87[ASN][1000 genomes]
rs62123700	0.87[ASN][1000 genomes]
rs6508902	1.00[CEU][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6508905	0.93[ASN][1000 genomes]
rs718798	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs718799	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7248546	0.83[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7257941	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73036596	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73036598	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7507315	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8100721	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8106628	0.96[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8109921	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8110945	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8112007	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs978671	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057361	chr19:40123868-40310996	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv1061361	chr19:40131820-40310996	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv579511	chr19:40132825-40310497	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv1062394	chr19:40133229-40310186	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv544004	chr19:40133229-40310186	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv1059691	chr19:40168862-40306373	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv544005	chr19:40168862-40306373	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	esv3332670	chr19:40181720-40297955	Active TSS Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	esv3329492	chr19:40198535-40437035	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
10	nsv911695	chr19:40217794-40235008	Weak transcription Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	esv2758498	chr19:40227904-40521130	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
12	esv2758760	chr19:40227904-40521130	Genic enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
13	nsv428022	chr19:40227904-40521130	Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
14	nsv978750	chr19:40228783-40230366	Weak transcription Enhancers	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Schizophrenia	23894747	GWAS catalog

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12611334	CEACAM21	cis	parietal	SCAN
rs12611334	RTN2	cis	parietal	SCAN
rs12611334	DACT3	cis	parietal	SCAN
rs12611334	KLC3	cis	cerebellum	SCAN
rs12611334	ZNF222	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40227800-40229600	Enhancers	Primary T helper cells fromperipheralblood	blood
2	chr19:40228600-40230200	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr19:40228800-40230000	Enhancers	H1 Cell Line	embryonic stem cell
4	chr19:40228800-40230600	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr19:40228800-40231200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr19:40229200-40230600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr19:40229200-40230800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr19:40229200-40237400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr19:40229400-40229800	Enhancers	Monocytes-CD14+_RO01746	blood
10	chr19:40229400-40236200	Weak transcription	GM12878-XiMat	blood

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