Variant report

Variant	rs2288865
Chromosome Location	chr19:19763635-19763636
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:19757747..19759331-chr19:19762568..19765721,3	K562	blood:
2	chr19:19757212..19759308-chr19:19762231..19764306,2	K562	blood:
3	chr19:19736867..19738953-chr19:19762486..19765452,2	K562	blood:
4	chr19:19752883..19756107-chr19:19759212..19764518,8	MCF-7	breast:
5	chr19:19727841..19730107-chr19:19763060..19764845,2	MCF-7	breast:
6	chr19:19747876..19749863-chr19:19760954..19763735,2	K562	blood:
7	chr19:19639119..19641341-chr19:19760899..19763693,2	K562	blood:
8	chr19:19763223..19765065-chr19:19765114..19767818,2	MCF-7	breast:
9	chr19:19761051..19765216-chr19:19766866..19770824,5	K562	blood:

No data

Variant related genes	Relation type
ENSG00000105717	Chromatin interaction
ENSG00000064547	Chromatin interaction
ENSG00000250067	Chromatin interaction
ENSG00000105726	Chromatin interaction
ENSG00000089639	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10401926	0.88[CEU][hapmap];0.88[TSI][hapmap]
rs10405234	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10415278	0.88[CEU][hapmap];0.88[TSI][hapmap];0.87[YRI][hapmap]
rs10423311	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10423449	0.88[CEU][hapmap];0.86[TSI][hapmap];0.87[YRI][hapmap]
rs11667828	0.89[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11668721	0.88[CEU][hapmap];0.80[TSI][hapmap]
rs11670710	0.89[CEU][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.82[ASN][1000 genomes]
rs12974308	0.83[ASN][1000 genomes]
rs12976582	0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12980482	0.81[ASN][1000 genomes]
rs12982049	0.83[ASN][1000 genomes]
rs12982500	0.83[ASN][1000 genomes]
rs12983292	0.89[CEU][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1433079	0.99[ASN][1000 genomes]
rs16996227	0.82[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2288867	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]
rs28472726	0.89[AMR][1000 genomes]
rs28635562	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34558847	0.82[ASN][1000 genomes]
rs35035906	0.99[ASN][1000 genomes]
rs35445661	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs35449009	0.82[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs35792080	0.84[ASN][1000 genomes]
rs35801717	0.83[ASN][1000 genomes]
rs3752152	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3794996	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4808209	0.82[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4808975	0.82[EUR][1000 genomes]
rs4808976	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4808979	0.81[ASN][1000 genomes]
rs4808981	0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7247142	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7249670	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7251924	0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7253821	0.81[CEU][hapmap];0.88[TSI][hapmap]
rs74181147	0.83[ASN][1000 genomes]
rs74181148	0.83[ASN][1000 genomes]
rs74181149	0.83[ASN][1000 genomes]
rs74181150	0.83[ASN][1000 genomes]
rs74181151	0.83[ASN][1000 genomes]
rs8107058	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs867616	0.88[CEU][hapmap];0.87[YRI][hapmap]
rs884480	0.88[CEU][hapmap];0.80[TSI][hapmap];0.87[YRI][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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2288865	EDG4	cis	multi-tissue	Pritchard
rs2288865	ZNF738	cis	cerebellum	SCAN
rs2288865	ZNF14	cis	parietal	SCAN
rs2288865	UNC13A	cis	cerebellum	SCAN
rs2288865	C19orf60	cis	parietal	SCAN
rs2288865	OR10H4	cis	parietal	SCAN
rs2288865	ZNF14	cis	cerebellum	SCAN
rs2288865	SNORA68	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19754800-19764200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr19:19754800-19767200	Weak transcription	Fetal Brain Male	brain
3	chr19:19754800-19769000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr19:19754800-19772400	Weak transcription	Right Atrium	heart
5	chr19:19755000-19765600	Weak transcription	Hela-S3	cervix
6	chr19:19755000-19769600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr19:19755000-19770800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr19:19755000-19771000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr19:19755000-19771200	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr19:19755000-19771200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
11	chr19:19755000-19772000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr19:19755000-19772000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr19:19755000-19772200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr19:19755200-19763800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr19:19755200-19765800	Weak transcription	Fetal Kidney	kidney
16	chr19:19755200-19767200	Strong transcription	Fetal Brain Female	brain
17	chr19:19755200-19770600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr19:19755200-19770600	Strong transcription	Dnd41	blood
19	chr19:19755200-19770800	Strong transcription	Primary T helper cells PMA-I stimulated	--
20	chr19:19755200-19770800	Strong transcription	Adipose Nuclei	Adipose
21	chr19:19755200-19770800	Strong transcription	Brain Germinal Matrix	brain
22	chr19:19755200-19770800	Strong transcription	Fetal Intestine Large	intestine
23	chr19:19755200-19770800	Strong transcription	Spleen	Spleen
24	chr19:19755200-19771000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chr19:19755200-19771000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr19:19755200-19771000	Strong transcription	Fetal Lung	lung
27	chr19:19755200-19771000	Strong transcription	Placenta	Placenta
28	chr19:19755200-19771200	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr19:19755200-19771200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr19:19755200-19771200	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr19:19755200-19771600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr19:19755200-19771600	Strong transcription	Skeletal Muscle Male	skeletal muscle
33	chr19:19755200-19772200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr19:19755200-19772200	Strong transcription	Fetal Stomach	stomach
35	chr19:19755200-19772200	Strong transcription	NHEK	skin
36	chr19:19755200-19772400	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr19:19755400-19770600	Strong transcription	Primary B cells from peripheral blood	blood
38	chr19:19755400-19770800	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr19:19755400-19771000	Strong transcription	Osteobl	bone
40	chr19:19755400-19771200	Strong transcription	Fetal Thymus	thymus
41	chr19:19755400-19771200	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr19:19755400-19772800	Strong transcription	Thymus	Thymus
43	chr19:19755600-19768200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr19:19755600-19770800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
45	chr19:19755600-19771000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr19:19755600-19771000	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr19:19755600-19771000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr19:19755600-19771000	Strong transcription	Liver	Liver
49	chr19:19755600-19771200	Strong transcription	H1 Cell Line	embryonic stem cell
50	chr19:19755600-19771200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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