Variant report

Variant	rs11668501
Chromosome Location	chr19:41228629-41228630
allele	C/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	chr19:41227762-41228664	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr19:41220314-41228780	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr19:41220376-41228744	MCF10A-Er-Src	breast:	n/a	n/a
4	STAT3	chr19:41228090-41228646	MCF10A-Er-Src	breast:	n/a	n/a
5	FOS	chr19:41227965-41228635	HUVEC	blood vessel:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr19:41219786..41224599-chr19:41225550..41230033,6	K562	blood:
2	chr19:41227271..41230078-chr19:41282801..41284516,2	MCF-7	breast:
3	chr19:41220671..41224766-chr19:41226443..41229963,4	K562	blood:
4	chr19:41228463..41230519-chr19:41256457..41258245,2	MCF-7	breast:
5	chr19:41224979..41226592-chr19:41227722..41229766,2	K562	blood:
6	chr19:41168010..41170261-chr19:41227028..41229783,2	MCF-7	breast:
7	chr19:41226837..41229438-chr19:41260513..41263205,2	MCF-7	breast:
8	chr19:41196019..41197833-chr19:41228097..41229742,2	MCF-7	breast:

No data

Variant related genes	Relation type
ADCK4	TF binding region
ENSG00000086544	Chromatin interaction
ENSG00000123815	Chromatin interaction
ENSG00000105245	Chromatin interaction
ENSG00000171570	Chromatin interaction
ENSG00000188493	Chromatin interaction
ENSG00000167578	Chromatin interaction
ENSG00000077312	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11665867	0.87[ASW][hapmap];0.96[LWK][hapmap]
rs11671127	0.94[EUR][1000 genomes]
rs11673492	1.00[ASW][hapmap];0.94[CEU][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12975396	0.89[ASW][hapmap];0.96[LWK][hapmap]
rs12983335	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12984298	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4420642	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55993576	1.00[ASN][1000 genomes]
rs66599479	1.00[ASN][1000 genomes]
rs66743282	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs66865752	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs67083521	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7249805	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7253502	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7253804	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8105009	1.00[ASW][hapmap];0.92[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1830682	chr19:40880127-41270055	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	139 gene(s)	inside rSNPs	diseases
2	esv1800615	chr19:41127465-41270055	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	nsv1067017	chr19:41185992-41231251	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11668501	FOXA3	cis	parietal	SCAN
rs11668501	STRN4	cis	parietal	SCAN
rs11668501	APOC4	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41225200-41229200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr19:41225200-41229400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr19:41225200-41235200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr19:41225200-41238800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr19:41225200-41243200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr19:41225400-41231000	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr19:41225600-41229800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr19:41225600-41231600	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr19:41225800-41229600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr19:41225800-41229800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr19:41225800-41229800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr19:41225800-41229800	Weak transcription	Thymus	Thymus
13	chr19:41225800-41232000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr19:41225800-41232200	Weak transcription	Fetal Kidney	kidney
15	chr19:41225800-41233400	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr19:41225800-41233400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr19:41225800-41236400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr19:41226400-41228800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr19:41226400-41229600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr19:41226400-41246200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr19:41226600-41228800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr19:41226600-41229200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr19:41226600-41238600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr19:41226600-41245600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr19:41226800-41228800	Genic enhancers	Placenta Amnion	Placenta Amnion
26	chr19:41226800-41229800	Weak transcription	Primary T cells from cord blood	blood
27	chr19:41226800-41230000	Weak transcription	HSMMtube	muscle
28	chr19:41226800-41236600	Weak transcription	GM12878-XiMat	blood
29	chr19:41226800-41245200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr19:41226800-41245600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr19:41226800-41245800	Strong transcription	Fetal Stomach	stomach
32	chr19:41227000-41254600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr19:41227200-41228800	Enhancers	Skeletal Muscle Male	skeletal muscle
34	chr19:41227200-41229000	Genic enhancers	Placenta	Placenta
35	chr19:41227200-41229200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr19:41227200-41229400	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr19:41227200-41229600	Weak transcription	Fetal Lung	lung
38	chr19:41227200-41229600	Weak transcription	Ovary	ovary
39	chr19:41227200-41229800	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr19:41227200-41229800	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr19:41227200-41229800	Weak transcription	Brain Germinal Matrix	brain
42	chr19:41227200-41229800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr19:41227200-41229800	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr19:41227200-41229800	Weak transcription	NHLF	lung
45	chr19:41227200-41231000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr19:41227200-41231000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr19:41227200-41231200	Weak transcription	Aorta	Aorta
48	chr19:41227200-41232200	Weak transcription	K562	blood
49	chr19:41227200-41237000	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr19:41227200-41255200	Weak transcription	Fetal Heart	heart

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