Variant report

Variant	rs2079646
Chromosome Location	chr19:44137982-44137983
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:44131324..44133341-chr19:44135623..44138408,2	K562	blood:
2	chr19:44118551..44131201-chr19:44135615..44147023,20	K562	blood:
3	chr19:44137719..44140968-chr19:44143779..44146141,3	K562	blood:
4	chr19:44122314..44129769-chr19:44133350..44139066,11	MCF-7	breast:
5	chr19:44100944..44102513-chr19:44136939..44138687,2	MCF-7	breast:
6	chr19:44137846..44140396-chr19:44141392..44144288,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000131116	Chromatin interaction
ENSG00000105767	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11083712	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11671645	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12461175	1.00[CEU][hapmap];0.84[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1402325	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[GIH][hapmap];0.83[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1402326	1.00[CEU][hapmap];0.84[GIH][hapmap];0.84[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17655574	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs1879387	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2003098	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2302421	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[GIH][hapmap];0.84[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3746002	0.85[CEU][hapmap];0.82[CHB][hapmap];0.84[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3746003	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.92[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3815422	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4803643	0.88[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4803644	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4803648	0.90[JPT][hapmap]
rs7252391	0.85[CHD][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs73038867	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs767540	1.00[CEU][hapmap];0.87[MEX][hapmap]
rs880108	1.00[CEU][hapmap];0.84[GIH][hapmap];0.83[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.94[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	nsv532821	chr19:43842383-44357315	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv833839	chr19:44099813-44272299	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2079646	PLAUR	cis	multi-tissue	Pritchard
rs2079646	ZNF615	cis	cerebellum	SCAN
rs2079646	PRRG2	cis	cerebellum	SCAN
rs2079646	IZUMO2	cis	parietal	SCAN
rs2079646	ZNF480	cis	parietal	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44124600-44143400	Weak transcription	Right Atrium	heart
2	chr19:44124800-44138400	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr19:44124800-44138800	Weak transcription	Rectal Smooth Muscle	rectum
4	chr19:44124800-44139000	Weak transcription	Colon Smooth Muscle	Colon
5	chr19:44125000-44139200	Weak transcription	Pancreas	Pancrea
6	chr19:44128600-44138800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr19:44129000-44138400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr19:44129200-44138200	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr19:44130800-44138400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr19:44131000-44138800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr19:44131200-44138200	Weak transcription	Esophagus	oesophagus
12	chr19:44131200-44139400	Weak transcription	Spleen	Spleen
13	chr19:44131400-44138400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr19:44131400-44138400	Weak transcription	Fetal Stomach	stomach
15	chr19:44131400-44138800	Weak transcription	Fetal Intestine Small	intestine
16	chr19:44131600-44138200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr19:44131600-44138400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr19:44131800-44138800	Weak transcription	Stomach Smooth Muscle	stomach
19	chr19:44131800-44139000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr19:44132000-44138400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr19:44132000-44138800	Weak transcription	K562	blood
22	chr19:44133600-44138000	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr19:44133600-44138200	Weak transcription	Brain Angular Gyrus	brain
24	chr19:44133600-44138200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr19:44133800-44138000	Weak transcription	Brain Hippocampus Middle	brain
26	chr19:44135200-44138200	Weak transcription	Fetal Brain Female	brain
27	chr19:44135400-44138200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr19:44136200-44138000	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr19:44136600-44138200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr19:44136600-44138400	Weak transcription	Brain Germinal Matrix	brain
31	chr19:44136800-44138000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr19:44137000-44139000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr19:44137400-44138800	Enhancers	HepG2	liver
34	chr19:44137400-44142600	Enhancers	Fetal Brain Male	brain
35	chr19:44137600-44138000	Weak transcription	Brain Cingulate Gyrus	brain
36	chr19:44137600-44138200	Enhancers	Brain Anterior Caudate	brain
37	chr19:44137600-44138800	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr19:44137800-44138200	Enhancers	Brain Substantia Nigra	brain
39	chr19:44137800-44138200	Enhancers	HMEC	breast

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