Variant report

Variant	rs621469
Chromosome Location	chr19:53017217-53017218
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr19:53017206-53017403	K562	blood:	n/a	n/a
2	SPI1	chr19:53017125-53017515	HL-60	blood:	n/a	n/a
3	SPI1	chr19:53017088-53017464	HL-60	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000269349	TF binding region

Extended variants
information (count: 49 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11084170	0.88[ASN][1000 genomes]
rs11669969	0.87[ASN][1000 genomes]
rs12610532	0.94[ASN][1000 genomes]
rs12984325	0.87[ASN][1000 genomes]
rs161930	0.85[CEU][hapmap];0.82[CHD][hapmap]
rs161932	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1677467	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs172956	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2011702	0.87[ASN][1000 genomes]
rs2115372	0.81[ASN][1000 genomes]
rs2868688	0.80[ASN][1000 genomes]
rs324745	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324747	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs324748	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs326441	0.82[JPT][hapmap]
rs326449	0.82[JPT][hapmap]
rs326452	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs326456	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs326458	0.83[JPT][hapmap]
rs329929	0.83[ASN][1000 genomes]
rs329930	0.81[ASN][1000 genomes]
rs378790	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs389503	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs400278	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs414595	0.99[ASN][1000 genomes]
rs414804	0.89[ASN][1000 genomes]
rs419317	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4802968	0.94[ASN][1000 genomes]
rs4802969	0.90[ASN][1000 genomes]
rs4802970	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs633763	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs650885	0.91[ASN][1000 genomes]
rs650937	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs666356	0.80[JPT][hapmap]
rs802878	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	nsv1066537	chr19:52794424-53044977	Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv544060	chr19:52794424-53044977	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv580026	chr19:52937100-53059872	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1063648	chr19:52938131-53041119	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1057296	chr19:52950339-53396986	Weak transcription Active TSS ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv978841	chr19:52983057-53088237	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	esv3404701	chr19:52986895-53035152	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1058567	chr19:52992455-53021505	Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases
9	esv3440535	chr19:52993529-53035203	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1066717	chr19:52993620-53041995	Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv1064342	chr19:52996710-53041119	ZNF genes & repeats Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv1055825	chr19:53001299-53037378	Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv1055859	chr19:53001299-53041119	Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	nsv1060656	chr19:53001299-53041995	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs621469	NLRP12	cis	cerebellum	SCAN
rs621469	BRSK1	cis	parietal	SCAN
rs621469	PPP1R12C	cis	cerebellum	SCAN
rs621469	ZSCAN18	cis	cerebellum	SCAN
rs621469	ISOC2	cis	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53002600-53021400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr19:53003400-53022600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr19:53003800-53017600	Weak transcription	Fetal Muscle Trunk	muscle
4	chr19:53006400-53021200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr19:53006400-53021400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr19:53006800-53021400	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr19:53007000-53021400	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr19:53009000-53022600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr19:53011000-53017800	Weak transcription	Right Ventricle	heart
10	chr19:53013200-53021800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr19:53013800-53018200	Strong transcription	Fetal Muscle Leg	muscle
12	chr19:53014800-53021200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr19:53015000-53020600	Strong transcription	Fetal Brain Female	brain
14	chr19:53015400-53018400	Weak transcription	Dnd41	blood
15	chr19:53015400-53029600	Weak transcription	Fetal Brain Male	brain
16	chr19:53015600-53017400	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr19:53015600-53017600	Weak transcription	HSMMtube	muscle
18	chr19:53015600-53017800	Weak transcription	Fetal Kidney	kidney
19	chr19:53015600-53017800	Weak transcription	Fetal Lung	lung
20	chr19:53015600-53018400	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr19:53015600-53018600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr19:53015600-53019200	Weak transcription	Brain Angular Gyrus	brain
23	chr19:53015600-53021200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr19:53015800-53021400	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr19:53016400-53030000	Weak transcription	Brain Germinal Matrix	brain
26	chr19:53017000-53020200	Weak transcription	Ovary	ovary
27	chr19:53017200-53018800	Weak transcription	Fetal Stomach	stomach
28	chr19:53017200-53020200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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