Variant report

Variant	rs12976664
Chromosome Location	chr19:39659486-39659487
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:39572549..39576644-chr19:39655893..39659798,4	MCF-7	breast:
2	chr19:39614796..39618723-chr19:39655193..39659848,7	MCF-7	breast:
3	chr19:39656758..39659351-chr19:39659366..39664473,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000183760	Chromatin interaction
ENSG00000130669	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	0.85[EUR][1000 genomes]
rs12977799	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1549927	0.90[EUR][1000 genomes]
rs476713	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4803208	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs490249	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs513053	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs529336	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs550664	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs554114	0.84[EUR][1000 genomes]
rs576527	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs691080	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs691577	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs692191	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs692257	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs692337	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs692468	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs692475	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[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
rs12976664	PAK4	cis	Thyroid	GTEx

Chromatin state (count:111 , 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	chr19:39631000-39660000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr19:39636000-39668200	Weak transcription	Primary B cells from cord blood	blood
4	chr19:39636400-39665600	Weak transcription	Aorta	Aorta
5	chr19:39637400-39660800	Weak transcription	Primary hematopoietic stem cells	blood
6	chr19:39638000-39661400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr19:39640000-39672600	Weak transcription	GM12878-XiMat	blood
8	chr19:39640200-39660000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr19:39646800-39660600	Weak transcription	Dnd41	blood
10	chr19:39647200-39660400	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr19:39647600-39660600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr19:39647600-39664800	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr19:39647800-39670400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr19:39649800-39659800	Weak transcription	Primary T cells from cord blood	blood
15	chr19:39651800-39660600	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr19:39651800-39660800	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr19:39652000-39659600	Weak transcription	NHLF	lung
18	chr19:39652000-39660400	Weak transcription	Adipose Nuclei	Adipose
19	chr19:39652000-39660600	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr19:39652000-39660800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr19:39652200-39661000	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr19:39652400-39660000	Weak transcription	Osteobl	bone
23	chr19:39652400-39661000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr19:39652600-39660600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr19:39653800-39663200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr19:39654000-39660000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr19:39654000-39660600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr19:39654000-39661400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr19:39654200-39674000	Weak transcription	K562	blood
30	chr19:39656600-39664800	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr19:39656800-39660400	Weak transcription	Small Intestine	intestine
32	chr19:39657000-39660000	Enhancers	H1 Cell Line	embryonic stem cell
33	chr19:39657200-39659800	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr19:39657200-39667200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr19:39657400-39659800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr19:39657600-39660600	Weak transcription	Primary B cells from peripheral blood	blood
37	chr19:39657800-39659600	Weak transcription	Fetal Brain Female	brain
38	chr19:39657800-39659600	Enhancers	HepG2	liver
39	chr19:39657800-39663000	Weak transcription	Rectal Smooth Muscle	rectum
40	chr19:39657800-39687600	Weak transcription	Right Atrium	heart
41	chr19:39658000-39660200	Weak transcription	Left Ventricle	heart
42	chr19:39658000-39660600	Weak transcription	Liver	Liver
43	chr19:39658000-39661400	Weak transcription	Brain Substantia Nigra	brain
44	chr19:39658000-39666600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr19:39658200-39660200	Weak transcription	Fetal Thymus	thymus
46	chr19:39658200-39660600	Weak transcription	Colon Smooth Muscle	Colon
47	chr19:39658200-39660600	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr19:39658200-39660600	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr19:39658200-39660800	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr19:39658400-39659600	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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