Variant report

Variant	rs879689
Chromosome Location	chr19:39650830-39650831
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:39649335..39651223-chr19:39816830..39818600,2	MCF-7	breast:
2	chr19:39643758..39646287-chr19:39649616..39652008,3	K562	blood:
3	chr19:39649401..39653814-chr19:39654605..39660099,7	K562	blood:
4	chr19:39615259..39630637-chr19:39640467..39653924,38	MCF-7	breast:

Variant related genes	Relation type
ENSG00000130669	Chromatin interaction
ENSG00000269172	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11083508	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[GIH][hapmap];0.81[JPT][hapmap]
rs11666140	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11666238	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11669124	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs11671084	0.96[CEU][hapmap];0.82[CHB][hapmap]
rs11672886	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11673014	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12972566	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13228	0.96[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17641276	0.84[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.81[JPT][hapmap];0.82[TSI][hapmap]
rs17708461	0.96[CEU][hapmap];0.86[CHB][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2304090	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2319152	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35946542	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4803207	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4803209	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4803212	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59944493	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs750247	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs754703	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs754704	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8101281	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8101444	0.81[ASN][1000 genomes]
rs8105289	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs874535	1.00[CEU][hapmap];0.95[CHB][hapmap];0.80[JPT][hapmap];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833829	chr19:39569681-39730777	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv432048	chr19:39572060-39850060	Bivalent/Poised TSS Bivalent Enhancer Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs879689	PAK4	cis	Whole Blood	GTEx
rs879689	PAK4	cis	Thyroid	GTEx
rs879689	PAK4	cis	Skin Sun Exposed Lower leg	GTEx
rs879689	CNFN	cis	cerebellum	SCAN
rs879689	CRX	cis	parietal	SCAN
rs879689	PAK4	cis	Adipose Subcutaneous	GTEx
rs879689	B9D2	cis	cerebellum	SCAN
rs879689	B3GNT8	cis	cerebellum	SCAN

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39617400-39659800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr19:39630800-39651000	Weak transcription	NHDF-Ad	bronchial
3	chr19:39631000-39660000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr19:39636000-39668200	Weak transcription	Primary B cells from cord blood	blood
5	chr19:39636400-39665600	Weak transcription	Aorta	Aorta
6	chr19:39637000-39653600	Weak transcription	Brain Germinal Matrix	brain
7	chr19:39637400-39660800	Weak transcription	Primary hematopoietic stem cells	blood
8	chr19:39638000-39661400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr19:39640000-39672600	Weak transcription	GM12878-XiMat	blood
10	chr19:39640200-39660000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr19:39644200-39652200	Enhancers	Placenta Amnion	Placenta Amnion
12	chr19:39644400-39651800	Genic enhancers	Fetal Intestine Small	intestine
13	chr19:39644600-39652200	Enhancers	Stomach Mucosa	stomach
14	chr19:39644800-39652400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr19:39645200-39659000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr19:39645400-39654600	Enhancers	Ovary	ovary
17	chr19:39645800-39658000	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr19:39646600-39652200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr19:39646600-39653200	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr19:39646600-39659000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr19:39646800-39659200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr19:39646800-39660600	Weak transcription	Dnd41	blood
23	chr19:39647200-39660400	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr19:39647400-39651800	Genic enhancers	Spleen	Spleen
25	chr19:39647600-39653400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr19:39647600-39653400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr19:39647600-39660600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr19:39647600-39664800	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr19:39647800-39651000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr19:39647800-39653400	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr19:39647800-39653600	Weak transcription	Fetal Thymus	thymus
32	chr19:39647800-39670400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr19:39648200-39651000	Weak transcription	HSMMtube	muscle
34	chr19:39648200-39651200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr19:39648600-39652600	Genic enhancers	Fetal Stomach	stomach
36	chr19:39648800-39651600	Weak transcription	Brain Cingulate Gyrus	brain
37	chr19:39648800-39653600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr19:39648800-39653600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr19:39649000-39651000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr19:39649000-39651000	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr19:39649000-39651000	Weak transcription	Colonic Mucosa	Colon
42	chr19:39649000-39651000	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr19:39649000-39651000	Weak transcription	HSMM	muscle
44	chr19:39649000-39651200	Weak transcription	Brain Anterior Caudate	brain
45	chr19:39649000-39651200	Strong transcription	Thymus	Thymus
46	chr19:39649000-39651400	Weak transcription	Brain Angular Gyrus	brain
47	chr19:39649000-39651600	Genic enhancers	Fetal Muscle Trunk	muscle
48	chr19:39649000-39651800	Weak transcription	Right Atrium	heart
49	chr19:39649000-39657400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr19:39649200-39651600	Strong transcription	Fetal Brain Female	brain

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