Variant report

Variant	rs513053
Chromosome Location	chr19:39641146-39641147
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:39638971..39643610-chr19:39643688..39647493,10	MCF-7	breast:
2	chr19:39631951..39634842-chr19:39640711..39642927,2	MCF-7	breast:
3	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: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12976130	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs12976664	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12977799	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1549927	0.85[CEU][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs476713	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4803208	0.81[CEU][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs490249	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs529336	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs550664	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs554114	0.84[EUR][1000 genomes]
rs576527	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs691080	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs691577	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs692191	1.00[ASW][hapmap];0.81[CEU][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs692257	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs692337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs692468	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs692475	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs513053	PAK4	cis	Thyroid	GTEx

Chromatin state (count:108 , 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	chr19:39617800-39641600	Weak transcription	Thymus	Thymus
3	chr19:39618400-39646600	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr19:39623400-39646000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr19:39624000-39647000	Weak transcription	NHLF	lung
6	chr19:39627200-39646800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr19:39627600-39641200	Weak transcription	Hela-S3	cervix
8	chr19:39627600-39645800	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr19:39630800-39646800	Weak transcription	Osteobl	bone
10	chr19:39630800-39651000	Weak transcription	NHDF-Ad	bronchial
11	chr19:39631000-39660000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr19:39631800-39644600	Weak transcription	Primary T cells from cord blood	blood
13	chr19:39635400-39645600	Weak transcription	Spleen	Spleen
14	chr19:39635400-39647000	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr19:39635600-39647000	Weak transcription	NH-A	brain
16	chr19:39635600-39647400	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr19:39635800-39642800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr19:39635800-39646000	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr19:39636000-39647400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr19:39636000-39668200	Weak transcription	Primary B cells from cord blood	blood
21	chr19:39636200-39644800	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr19:39636400-39642000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr19:39636400-39645000	Weak transcription	Adipose Nuclei	Adipose
24	chr19:39636400-39665600	Weak transcription	Aorta	Aorta
25	chr19:39636800-39644600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr19:39636800-39644600	Weak transcription	HMEC	breast
27	chr19:39636800-39650800	Weak transcription	HUVEC	blood vessel
28	chr19:39637000-39641200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr19:39637000-39641600	Weak transcription	Right Atrium	heart
30	chr19:39637000-39641600	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr19:39637000-39643200	Weak transcription	Esophagus	oesophagus
32	chr19:39637000-39644600	Weak transcription	Colonic Mucosa	Colon
33	chr19:39637000-39644600	Weak transcription	Fetal Kidney	kidney
34	chr19:39637000-39644600	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr19:39637000-39645400	Weak transcription	Right Ventricle	heart
36	chr19:39637000-39653600	Weak transcription	Brain Germinal Matrix	brain
37	chr19:39637200-39644800	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr19:39637200-39647000	Weak transcription	Small Intestine	intestine
39	chr19:39637400-39644400	Weak transcription	Pancreas	Pancrea
40	chr19:39637400-39644600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr19:39637400-39644600	Weak transcription	Duodenum Mucosa	Duodenum
42	chr19:39637400-39644600	Weak transcription	Stomach Mucosa	stomach
43	chr19:39637400-39645800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr19:39637400-39647400	Weak transcription	Rectal Smooth Muscle	rectum
45	chr19:39637400-39660800	Weak transcription	Primary hematopoietic stem cells	blood
46	chr19:39637600-39645200	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr19:39637800-39644600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr19:39638000-39644600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr19:39638000-39645400	Weak transcription	Stomach Smooth Muscle	stomach
50	chr19:39638000-39646000	Weak transcription	Colon Smooth Muscle	Colon

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