Variant report

Variant	rs11882744
Chromosome Location	chr19:39973024-39973025
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:39947157-39987373	PANC-1	pancreas:	n/a	n/a
2	MYC	chr19:39970732-39973093	A549	lung:	n/a	chr19:39971808-39971823 chr19:39971812-39971822 chr19:39971811-39971821
3	SIN3AK20	chr19:39970475-39973057	PANC-1	pancreas:	n/a	n/a
4	ESRRA	chr19:39970619-39973183	GM12878	blood:	n/a	chr19:39972390-39972403
5	SIN3AK20	chr19:39970208-39973088	PANC-1	pancreas:	n/a	n/a
6	REST	chr19:39970787-39973063	PANC-1	pancreas:	n/a	chr19:39971694-39971708

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39970388..39973416-chr19:39987093..39991960,6	MCF-7	breast:
2	chr19:39881392..39883533-chr19:39972449..39976025,3	K562	blood:
3	chr19:39971121..39973511-chr19:39973741..39976891,3	MCF-7	breast:
4	chr19:39923294..39928217-chr19:39969939..39976745,7	K562	blood:
5	chr19:39934676..39937838-chr19:39970025..39973557,7	MCF-7	breast:
6	chr19:39924549..39928313-chr19:39970394..39973544,4	MCF-7	breast:
7	chr19:39971313..39973393-chr19:39989065..39991077,2	MCF-7	breast:
8	chr19:39956900..39963294-chr19:39968062..39973681,7	MCF-7	breast:
9	chr19:39965047..39968880-chr19:39971509..39974367,5	MCF-7	breast:
10	chr19:39960496..39962184-chr19:39970692..39973089,3	MCF-7	breast:
11	chr19:39925979..39927964-chr19:39971323..39973932,2	K562	blood:

No data

Variant related genes	Relation type
TIMM50	TF binding region
ENSG00000063322	Chromatin interaction
ENSG00000196235	Chromatin interaction
ENSG00000105197	Chromatin interaction
ENSG00000105193	Chromatin interaction
ENSG00000006712	Chromatin interaction
ENSG00000090932	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10420073	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10423161	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10423921	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10425652	0.91[CHB][hapmap];0.86[CHD][hapmap];0.82[ASN][1000 genomes]
rs10426543	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1529733	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1865094	0.84[GIH][hapmap]
rs3786950	0.91[CHB][hapmap];0.82[ASN][1000 genomes]
rs45568533	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4802030	0.94[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.88[YRI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4802033	0.95[CHB][hapmap];0.86[CHD][hapmap];0.84[ASN][1000 genomes]
rs4803238	1.00[CEU][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.95[TSI][hapmap]
rs4803241	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs4803244	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4803248	0.84[ASN][1000 genomes]
rs59269050	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61480418	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62120691	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7245986	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7246329	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73035459	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73035461	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8106642	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911689	chr19:39903088-40021759	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	nsv911690	chr19:39903088-40046863	Weak transcription Bivalent Enhancer Strong transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	nsv523856	chr19:39913558-39997472	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
4	nsv544003	chr19:39937078-39974282	Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11882744	B3GNT8	cis	parietal	SCAN
rs11882744	PRKD2	cis	cerebellum	SCAN
rs11882744	CD177	cis	parietal	SCAN
rs11882744	MIA	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39972200-39986400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:39972400-39973400	Enhancers	Spleen	Spleen
3	chr19:39972400-39976400	Weak transcription	Aorta	Aorta
4	chr19:39972600-39973400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr19:39972600-39973400	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr19:39972600-39973600	Enhancers	Primary T cells fromperipheralblood	blood
7	chr19:39972600-39973600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr19:39972600-39973600	Enhancers	Primary T killer memory cells from peripheral blood	blood
9	chr19:39972600-39975000	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr19:39972600-39975200	Weak transcription	Small Intestine	intestine
11	chr19:39972600-39976000	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr19:39972600-39976200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr19:39972600-39976200	Weak transcription	Psoas Muscle	Psoas
14	chr19:39972600-39976400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr19:39972800-39973200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr19:39972800-39973200	Enhancers	Liver	Liver
17	chr19:39972800-39973200	Weak transcription	Fetal Muscle Leg	muscle
18	chr19:39972800-39973400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr19:39972800-39973400	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr19:39972800-39973400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr19:39972800-39973400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr19:39972800-39973400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr19:39972800-39973400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr19:39972800-39973400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr19:39972800-39973400	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr19:39972800-39973400	Weak transcription	Primary T cells from cord blood	blood
27	chr19:39972800-39973400	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr19:39972800-39973400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr19:39972800-39973400	Weak transcription	Brain Germinal Matrix	brain
30	chr19:39972800-39973400	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr19:39972800-39973400	Weak transcription	Thymus	Thymus
32	chr19:39972800-39973400	Weak transcription	NHLF	lung
33	chr19:39972800-39973600	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr19:39972800-39973600	Enhancers	Primary T helper cells PMA-I stimulated	--
35	chr19:39972800-39973600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr19:39972800-39973600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr19:39972800-39973600	Weak transcription	Adipose Nuclei	Adipose
38	chr19:39972800-39973600	Genic enhancers	Fetal Muscle Trunk	muscle
39	chr19:39972800-39973600	Weak transcription	Placenta	Placenta
40	chr19:39972800-39973600	Weak transcription	Lung	lung
41	chr19:39972800-39973600	Enhancers	Skeletal Muscle Female	skeletal muscle
42	chr19:39972800-39973600	Weak transcription	Stomach Smooth Muscle	stomach
43	chr19:39972800-39973600	Genic enhancers	K562	blood
44	chr19:39972800-39973800	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr19:39972800-39973800	Enhancers	GM12878-XiMat	blood
46	chr19:39972800-39974200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr19:39972800-39974200	Weak transcription	Left Ventricle	heart
48	chr19:39972800-39974200	Weak transcription	NH-A	brain
49	chr19:39972800-39974800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr19:39972800-39974800	Weak transcription	Osteobl	bone

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