Variant report

Variant	rs12976130
Chromosome Location	chr19:39625800-39625801
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:39619372..39620875-chr19:39624285..39626260,2	K562	blood:
2	chr19:39624151..39625876-chr19:39627199..39629585,2	K562	blood:
3	chr19:39615259..39630637-chr19:39640467..39653924,38	MCF-7	breast:
4	chr19:39622591..39626006-chr19:39627126..39631368,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SYCN-1	chr19:39625522-39625844	ENSG00000269172.1

Variant related genes	Relation type
ENSG00000130669	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs12976664	0.85[EUR][1000 genomes]
rs12977799	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1549927	0.88[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs476713	0.85[EUR][1000 genomes]
rs4803208	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs490249	0.85[EUR][1000 genomes]
rs513053	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs529336	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs550664	0.84[EUR][1000 genomes]
rs554114	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs576527	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs691080	0.85[EUR][1000 genomes]
rs691577	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs692191	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs692257	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs692337	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs692468	0.85[EUR][1000 genomes]
rs692475	0.81[CEU][hapmap];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv458571	chr19:39533754-39628050	Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv579508	chr19:39533754-39628050	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	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
4	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
5	esv2545161	chr19:39624402-39625800	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12976130	PAK4	cis	Thyroid	GTEx

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39617000-39630800	Weak transcription	Primary T cells from cord blood	blood
2	chr19:39617000-39635000	Weak transcription	Aorta	Aorta
3	chr19:39617400-39659800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr19:39617600-39627600	Enhancers	Fetal Heart	heart
5	chr19:39617800-39627200	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr19:39617800-39628600	Enhancers	Placenta	Placenta
7	chr19:39617800-39630200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr19:39617800-39641600	Weak transcription	Thymus	Thymus
9	chr19:39618200-39628400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr19:39618400-39626800	Weak transcription	NHEK	skin
11	chr19:39618400-39646600	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr19:39620000-39627200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr19:39620000-39630000	Weak transcription	HepG2	liver
14	chr19:39620600-39626800	Enhancers	Fetal Intestine Large	intestine
15	chr19:39621000-39627200	Enhancers	Fetal Lung	lung
16	chr19:39621000-39628400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr19:39621400-39628000	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr19:39621600-39627800	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr19:39621800-39627400	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr19:39622200-39627200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr19:39622200-39628200	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr19:39622400-39627000	Weak transcription	Small Intestine	intestine
23	chr19:39622400-39629000	Weak transcription	NH-A	brain
24	chr19:39622400-39635200	Weak transcription	Fetal Brain Female	brain
25	chr19:39622600-39639600	Weak transcription	HSMM	muscle
26	chr19:39622800-39626800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr19:39622800-39627400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr19:39623000-39635200	Weak transcription	Primary B cells from peripheral blood	blood
29	chr19:39623400-39626800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr19:39623400-39629000	Weak transcription	Brain Cingulate Gyrus	brain
31	chr19:39623400-39646000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr19:39623600-39626800	Weak transcription	Adipose Nuclei	Adipose
33	chr19:39623600-39627200	Weak transcription	HUVEC	blood vessel
34	chr19:39623600-39630200	Weak transcription	Brain Angular Gyrus	brain
35	chr19:39623800-39627400	Weak transcription	Brain Hippocampus Middle	brain
36	chr19:39623800-39630200	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr19:39624000-39647000	Weak transcription	NHLF	lung
38	chr19:39624200-39629000	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr19:39624200-39630200	Weak transcription	Rectal Smooth Muscle	rectum
40	chr19:39624200-39634800	Weak transcription	Fetal Kidney	kidney
41	chr19:39624400-39625800	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr19:39624400-39626400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr19:39624400-39626400	Weak transcription	A549	lung
44	chr19:39624400-39626800	Weak transcription	Brain Substantia Nigra	brain
45	chr19:39624400-39627000	Weak transcription	HMEC	breast
46	chr19:39624400-39627400	Weak transcription	Brain Germinal Matrix	brain
47	chr19:39624400-39628200	Enhancers	Rectal Mucosa Donor 31	rectum
48	chr19:39624400-39628600	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr19:39624400-39629000	Weak transcription	Right Ventricle	heart
50	chr19:39624400-39629000	Weak transcription	Skeletal Muscle Male	skeletal muscle

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