Variant report

Variant	rs11668309
Chromosome Location	chr19:55833460-55833461
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	ZNF263	chr19:55833099-55833510	HEK293-T-REx	kidney:	n/a	chr19:55833264-55833285 chr19:55833263-55833272

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:55831982..55833586-chr19:55834891..55837609,2	K562	blood:
2	chr19:55832067..55834529-chr19:55849640..55851865,2	K562	blood:

Variant related genes	Relation type
TMEM150B	TF binding region
ENSG00000133247	Chromatin interaction
ENSG00000267531	Chromatin interaction
ENSG00000180061	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10401201	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10411773	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10412726	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10420693	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10425848	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11084393	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1109368	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11668344	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1172821	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1172822	0.93[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11882930	0.97[ASN][1000 genomes]
rs1551562	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs2384686	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2384687	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2384688	0.97[ASN][1000 genomes]
rs2384689	0.97[ASN][1000 genomes]
rs2384690	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2384691	0.97[ASN][1000 genomes]
rs28875253	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34962991	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35515212	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4806659	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4806660	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4806661	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs734518	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7508682	0.95[ASN][1000 genomes]
rs8107664	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs897796	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs897797	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs897798	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][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	esv1816335	chr19:55683977-55901099	Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv1065760	chr19:55721521-55929740	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
3	nsv912455	chr19:55725410-55879872	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
4	nsv912456	chr19:55725410-55925500	Weak transcription Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
5	nsv912457	chr19:55725410-56019597	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	228 gene(s)	inside rSNPs	diseases
6	nsv912459	chr19:55791380-55845386	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
7	nsv432086	chr19:55807586-56050844	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	220 gene(s)	inside rSNPs	diseases
8	nsv912460	chr19:55814881-55897327	Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	99 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11668309	ZNF587	cis	cerebellum	SCAN
rs11668309	ZNF264	cis	cerebellum	SCAN
rs11668309	ZNF416	cis	parietal	SCAN
rs11668309	RPS5	cis	cerebellum	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:55813600-55850000	Weak transcription	Right Atrium	heart
2	chr19:55820800-55839000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr19:55828400-55833600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr19:55828600-55834400	Weak transcription	Lung	lung
5	chr19:55831400-55834600	Enhancers	Primary hematopoietic stem cells	blood
6	chr19:55831800-55834000	Weak transcription	K562	blood
7	chr19:55831800-55834600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr19:55831800-55835000	Enhancers	Adipose Nuclei	Adipose
9	chr19:55832000-55833800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr19:55832000-55834600	Enhancers	Stomach Mucosa	stomach
11	chr19:55832000-55836400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr19:55832400-55833600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr19:55832400-55834000	Enhancers	Fetal Thymus	thymus
14	chr19:55832400-55834000	Active TSS	Rectal Smooth Muscle	rectum
15	chr19:55832400-55834200	Flanking Active TSS	Colonic Mucosa	Colon
16	chr19:55832400-55834200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
17	chr19:55832400-55834600	Flanking Active TSS	Duodenum Mucosa	Duodenum
18	chr19:55832400-55834600	Flanking Active TSS	Fetal Intestine Large	intestine
19	chr19:55832400-55838600	Enhancers	Primary neutrophils fromperipheralblood	blood
20	chr19:55832600-55833800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr19:55832600-55833800	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
22	chr19:55832600-55834000	Enhancers	Spleen	Spleen
23	chr19:55832600-55834200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
24	chr19:55832800-55834600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
25	chr19:55832800-55834600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
26	chr19:55833000-55833800	Enhancers	Placenta	Placenta
27	chr19:55833000-55834600	Enhancers	A549	lung
28	chr19:55833000-55834800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
29	chr19:55833000-55835200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr19:55833200-55834200	Enhancers	HUES6 Cell Line	embryonic stem cell
31	chr19:55833200-55834200	Flanking Active TSS	Fetal Intestine Small	intestine
32	chr19:55833400-55833600	Enhancers	HUES64 Cell Line	embryonic stem cell
33	chr19:55833400-55833600	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr19:55833400-55833600	Enhancers	Small Intestine	intestine
35	chr19:55833400-55834000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr19:55833400-55834000	Enhancers	Primary hematopoietic stem cells short term culture	blood
37	chr19:55833400-55834000	Bivalent Enhancer	HepG2	liver
38	chr19:55833400-55834200	Enhancers	H1 Cell Line	embryonic stem cell

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