Variant report

Variant	rs4806661
Chromosome Location	chr19:55824661-55824662
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:55824030-55825180	K562	blood:	n/a	n/a
2	POLR2A	chr19:55824474-55824774	U87	brain:	n/a	n/a
3	POLR2A	chr19:55824032-55825550	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr19:55823921-55824869	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr19:55824171-55825239	H1-neurons	neurons:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:55823194..55826152-chr19:55862639..55864408,2	MCF-7	breast:
2	chr19:55823464..55826330-chr19:55895839..55897865,2	K562	blood:
3	chr19:55824405..55826212-chr19:56144765..56147267,2	K562	blood:
4	chr19:55824399..55826113-chr19:55831182..55832986,2	K562	blood:
5	chr19:55809710..55811444-chr19:55824368..55826135,2	K562	blood:
6	chr19:55819979..55821833-chr19:55824444..55826694,3	K562	blood:
7	chr19:55819947..55823832-chr19:55824271..55826603,6	K562	blood:
8	chr19:55822211..55824840-chr19:55897185..55900181,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000268729	TF binding region
ENSG00000213015	Chromatin interaction
ENSG00000108107	Chromatin interaction
ENSG00000233493	Chromatin interaction
ENSG00000171425	Chromatin interaction
ENSG00000160471	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	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];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	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10425848	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11084393	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1109368	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11668309	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]
rs11668344	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1172821	0.95[ASN][1000 genomes]
rs1172822	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]
rs11882930	1.00[ASN][1000 genomes]
rs1551562	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs2384686	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2384687	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2384688	1.00[ASN][1000 genomes]
rs2384689	1.00[ASN][1000 genomes]
rs2384690	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2384691	1.00[ASN][1000 genomes]
rs28875253	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34962991	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35515212	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4806659	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4806660	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.83[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	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs897796	0.97[AMR][1000 genomes];0.97[EUR][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: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
rs4806661	ZNF416	cis	parietal	SCAN
rs4806661	ZNF264	cis	cerebellum	SCAN
rs4806661	RPS5	cis	cerebellum	SCAN
rs4806661	ZNF587	cis	cerebellum	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:55813200-55825200	Weak transcription	Left Ventricle	heart
2	chr19:55813200-55827600	Weak transcription	Lung	lung
3	chr19:55813400-55825000	Strong transcription	Brain Germinal Matrix	brain
4	chr19:55813600-55824800	Strong transcription	Cortex derived primary cultured neurospheres	brain
5	chr19:55813600-55827400	Weak transcription	Rectal Smooth Muscle	rectum
6	chr19:55813600-55850000	Weak transcription	Right Atrium	heart
7	chr19:55813800-55827600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr19:55814000-55825200	Strong transcription	Fetal Brain Female	brain
9	chr19:55814000-55827600	Weak transcription	A549	lung
10	chr19:55814200-55825000	Strong transcription	Brain Inferior Temporal Lobe	brain
11	chr19:55814400-55831400	Weak transcription	Primary hematopoietic stem cells	blood
12	chr19:55817600-55824800	Weak transcription	K562	blood
13	chr19:55818200-55827400	Weak transcription	Aorta	Aorta
14	chr19:55818200-55832400	Weak transcription	Colonic Mucosa	Colon
15	chr19:55818400-55831000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr19:55818600-55831200	Weak transcription	Right Ventricle	heart
17	chr19:55820800-55839000	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr19:55821000-55831000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr19:55821000-55831200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr19:55821200-55824800	Weak transcription	Fetal Kidney	kidney
21	chr19:55821400-55825600	Weak transcription	Duodenum Mucosa	Duodenum
22	chr19:55821400-55825800	Strong transcription	Fetal Intestine Small	intestine
23	chr19:55821400-55827200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr19:55821400-55827600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr19:55821400-55831000	Weak transcription	Osteobl	bone
26	chr19:55821600-55825200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr19:55821600-55827400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr19:55821600-55827600	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr19:55821800-55829400	Weak transcription	NHLF	lung
30	chr19:55821800-55831000	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr19:55821800-55831000	Weak transcription	Fetal Brain Male	brain
32	chr19:55821800-55831200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr19:55822000-55824800	Weak transcription	HepG2	liver
34	chr19:55822000-55825600	Weak transcription	Colon Smooth Muscle	Colon
35	chr19:55822000-55825800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr19:55822000-55831000	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr19:55822000-55831400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr19:55822200-55831000	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr19:55822200-55831000	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr19:55822200-55831000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr19:55822200-55831000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr19:55822200-55831400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr19:55822200-55831400	Weak transcription	Brain Anterior Caudate	brain
44	chr19:55822200-55831400	Weak transcription	Brain Cingulate Gyrus	brain
45	chr19:55822200-55831400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr19:55822200-55831400	Weak transcription	Brain Substantia Nigra	brain
47	chr19:55822600-55824800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr19:55823000-55825000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr19:55823000-55825400	Genic enhancers	Fetal Stomach	stomach
50	chr19:55823200-55827400	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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