Variant report

Variant	rs2288867
Chromosome Location	chr19:19765568-19765569
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	POLR2A	chr19:19765309-19765877	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr19:19765201-19765648	K562	blood:	n/a	n/a
3	POLR2A	chr19:19765216-19765603	HepG2	liver:	n/a	n/a
4	POLR2A	chr19:19765236-19765636	GM12892	blood:	n/a	n/a
5	POLR2A	chr19:19765412-19765603	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:19757747..19759331-chr19:19762568..19765721,3	K562	blood:
2	chr19:19763223..19765065-chr19:19765114..19767818,2	MCF-7	breast:
3	chr19:19752450..19756333-chr19:19763709..19769200,7	K562	blood:

Variant related genes	Relation type
ATP13A1	TF binding region
ENSG00000105726	Chromatin interaction
ENSG00000089639	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10401926	0.83[CEU][hapmap];0.83[TSI][hapmap]
rs10405234	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10415278	0.83[CEU][hapmap];0.83[TSI][hapmap]
rs10421328	0.82[CEU][hapmap]
rs10423311	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10423449	0.83[CEU][hapmap];0.81[TSI][hapmap]
rs11667828	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.92[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11667844	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11668721	0.83[CEU][hapmap]
rs11670710	0.94[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12974308	0.82[ASN][1000 genomes]
rs12976582	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12982049	0.82[ASN][1000 genomes]
rs12982500	0.82[ASN][1000 genomes]
rs12983292	0.94[CEU][hapmap];0.83[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1433079	0.98[ASN][1000 genomes]
rs16996227	0.93[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2288865	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28635562	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34558847	0.81[ASN][1000 genomes]
rs35035906	0.98[ASN][1000 genomes]
rs35445661	0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs35449009	0.93[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs35792080	0.83[ASN][1000 genomes]
rs35801717	0.82[ASN][1000 genomes]
rs3752152	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3794996	0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4808209	0.93[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4808976	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808981	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs7249670	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7251924	0.82[ASN][1000 genomes]
rs7253821	0.83[TSI][hapmap]
rs74181147	0.82[ASN][1000 genomes]
rs74181148	0.82[ASN][1000 genomes]
rs74181149	0.82[ASN][1000 genomes]
rs74181150	0.82[ASN][1000 genomes]
rs74181151	0.82[ASN][1000 genomes]
rs8107058	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs867616	0.83[CEU][hapmap]
rs884480	0.83[CEU][hapmap]
rs919778	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1828240	chr19:19591146-19900900	Weak transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1063273	chr19:19591146-20061367	ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv911309	chr19:19727042-19784891	Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv911310	chr19:19753882-19784891	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases
5	esv3330851	chr19:19755507-19852881	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2288867	ZNF14	cis	parietal	SCAN
rs2288867	GMIP	cis	parietal	SCAN
rs2288867	UNC13A	cis	cerebellum	SCAN
rs2288867	C19orf60	cis	parietal	SCAN
rs2288867	SNORA68	cis	parietal	SCAN
rs2288867	ZNF14	cis	cerebellum	SCAN
rs2288867	MED26	cis	parietal	SCAN
rs2288867	OR10H4	cis	parietal	SCAN
rs2288867	ZNF738	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19754800-19767200	Weak transcription	Fetal Brain Male	brain
2	chr19:19754800-19769000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr19:19754800-19772400	Weak transcription	Right Atrium	heart
4	chr19:19755000-19765600	Weak transcription	Hela-S3	cervix
5	chr19:19755000-19769600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr19:19755000-19770800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr19:19755000-19771000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr19:19755000-19771200	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr19:19755000-19771200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
10	chr19:19755000-19772000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr19:19755000-19772000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr19:19755000-19772200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr19:19755200-19765800	Weak transcription	Fetal Kidney	kidney
14	chr19:19755200-19767200	Strong transcription	Fetal Brain Female	brain
15	chr19:19755200-19770600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr19:19755200-19770600	Strong transcription	Dnd41	blood
17	chr19:19755200-19770800	Strong transcription	Primary T helper cells PMA-I stimulated	--
18	chr19:19755200-19770800	Strong transcription	Adipose Nuclei	Adipose
19	chr19:19755200-19770800	Strong transcription	Brain Germinal Matrix	brain
20	chr19:19755200-19770800	Strong transcription	Fetal Intestine Large	intestine
21	chr19:19755200-19770800	Strong transcription	Spleen	Spleen
22	chr19:19755200-19771000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr19:19755200-19771000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr19:19755200-19771000	Strong transcription	Fetal Lung	lung
25	chr19:19755200-19771000	Strong transcription	Placenta	Placenta
26	chr19:19755200-19771200	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr19:19755200-19771200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr19:19755200-19771200	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr19:19755200-19771600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr19:19755200-19771600	Strong transcription	Skeletal Muscle Male	skeletal muscle
31	chr19:19755200-19772200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr19:19755200-19772200	Strong transcription	Fetal Stomach	stomach
33	chr19:19755200-19772200	Strong transcription	NHEK	skin
34	chr19:19755200-19772400	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr19:19755400-19770600	Strong transcription	Primary B cells from peripheral blood	blood
36	chr19:19755400-19770800	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr19:19755400-19771000	Strong transcription	Osteobl	bone
38	chr19:19755400-19771200	Strong transcription	Fetal Thymus	thymus
39	chr19:19755400-19771200	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr19:19755400-19772800	Strong transcription	Thymus	Thymus
41	chr19:19755600-19768200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr19:19755600-19770800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
43	chr19:19755600-19771000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr19:19755600-19771000	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr19:19755600-19771000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr19:19755600-19771000	Strong transcription	Liver	Liver
47	chr19:19755600-19771200	Strong transcription	H1 Cell Line	embryonic stem cell
48	chr19:19755600-19771200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr19:19755600-19771200	Strong transcription	Duodenum Mucosa	Duodenum
50	chr19:19755600-19771200	Strong transcription	Stomach Smooth Muscle	stomach

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