Variant report

Variant	rs1172822
Chromosome Location	chr19:55819845-55819846
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:55818918..55821375-chr19:55831220..55832903,2	MCF-7	breast:
2	chr19:55817946..55820760-chr19:55894289..55897191,2	K562	blood:
3	chr19:55819002..55821883-chr19:55917638..55919639,3	K562	blood:

Variant related genes	Relation type
ENSG00000233493	Chromatin interaction
ENSG00000180061	Chromatin interaction
ENSG00000108107	Chromatin interaction
ENSG00000108106	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs10401201	1.00[ASN][1000 genomes]
rs10411773	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10412726	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10420693	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10425848	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11084393	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1109368	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11668309	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]
rs11668344	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1172821	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11882930	1.00[ASN][1000 genomes]
rs1551562	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs2384686	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2384687	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2384688	1.00[ASN][1000 genomes]
rs2384689	1.00[ASN][1000 genomes]
rs2384690	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2384691	1.00[ASN][1000 genomes]
rs28875253	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34962991	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35515212	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4806659	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4806660	0.81[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4806661	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs734518	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7508682	0.97[ASN][1000 genomes]
rs8107664	0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs897796	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs897797	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs897798	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv912458	chr19:55763409-55823822	Active TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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

Variant related diseases (count:2)

Disease	PMID	Source
Menarche and menopause (age at onset)	19448621	GWAS catalog
Menopause (age at onset)	19448619	GWAS catalog

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1172822	ZNF264	cis	cerebellum	SCAN
rs1172822	RPS5	cis	cerebellum	SCAN
rs1172822	ZNF587	cis	cerebellum	SCAN
rs1172822	ZNF416	cis	parietal	SCAN

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:55797400-55824600	Weak transcription	Gastric	stomach
2	chr19:55813200-55825200	Weak transcription	Left Ventricle	heart
3	chr19:55813200-55827600	Weak transcription	Lung	lung
4	chr19:55813400-55821600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr19:55813400-55825000	Strong transcription	Brain Germinal Matrix	brain
6	chr19:55813600-55821200	Weak transcription	Pancreas	Pancrea
7	chr19:55813600-55821400	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr19:55813600-55822000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr19:55813600-55822400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr19:55813600-55824800	Strong transcription	Cortex derived primary cultured neurospheres	brain
11	chr19:55813600-55827400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr19:55813600-55850000	Weak transcription	Right Atrium	heart
13	chr19:55813800-55820400	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr19:55813800-55822000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr19:55813800-55822000	Strong transcription	Brain Hippocampus Middle	brain
16	chr19:55813800-55822600	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr19:55813800-55823200	Strong transcription	Brain Angular Gyrus	brain
18	chr19:55813800-55824000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr19:55813800-55824000	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr19:55813800-55824400	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr19:55813800-55827600	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr19:55814000-55821800	Strong transcription	H1 Cell Line	embryonic stem cell
23	chr19:55814000-55821800	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr19:55814000-55822200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
25	chr19:55814000-55822200	Strong transcription	Brain Cingulate Gyrus	brain
26	chr19:55814000-55822200	Strong transcription	Brain Substantia Nigra	brain
27	chr19:55814000-55822200	Strong transcription	Fetal Muscle Leg	muscle
28	chr19:55814000-55822400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr19:55814000-55823000	Strong transcription	Fetal Stomach	stomach
30	chr19:55814000-55824600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr19:55814000-55825200	Strong transcription	Fetal Brain Female	brain
32	chr19:55814000-55827600	Weak transcription	A549	lung
33	chr19:55814200-55821800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr19:55814200-55822000	Strong transcription	Stomach Smooth Muscle	stomach
35	chr19:55814200-55822200	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr19:55814200-55822200	Strong transcription	Brain Anterior Caudate	brain
37	chr19:55814200-55822200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr19:55814200-55825000	Strong transcription	Brain Inferior Temporal Lobe	brain
39	chr19:55814400-55820400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr19:55814400-55821600	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr19:55814400-55824600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr19:55814400-55831400	Weak transcription	Primary hematopoietic stem cells	blood
43	chr19:55815800-55820800	Weak transcription	HepG2	liver
44	chr19:55816600-55821200	Strong transcription	Fetal Kidney	kidney
45	chr19:55816800-55822400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr19:55817000-55822200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
47	chr19:55817000-55823000	Strong transcription	Fetal Muscle Trunk	muscle
48	chr19:55817400-55821000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
49	chr19:55817400-55822200	Strong transcription	HUES6 Cell Line	embryonic stem cell
50	chr19:55817600-55820800	Weak transcription	Fetal Thymus	thymus

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