Variant report

Variant	rs427115
Chromosome Location	chr19:44098197-44098198
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:44077678..44083171-chr19:44093489..44103015,14	K562	blood:
2	chr19:44095727..44098221-chr19:44098700..44101460,5	MCF-7	breast:
3	chr19:44082767..44086072-chr19:44097414..44100193,3	MCF-7	breast:
4	chr19:44097777..44104240-chr19:44121602..44130880,30	K562	blood:
5	chr19:44096922..44099842-chr19:44324178..44326451,2	K562	blood:
6	chr19:44063536..44067996-chr19:44097389..44100718,5	MCF-7	breast:
7	chr19:44097500..44104541-chr19:44116930..44130620,31	K562	blood:
8	chr19:44093767..44095435-chr19:44097697..44100110,2	MCF-7	breast:
9	chr19:44036790..44040633-chr19:44098075..44102401,5	K562	blood:

No data

Variant related genes	Relation type
ENSG00000176472	Chromatin interaction
ENSG00000124444	Chromatin interaction
ENSG00000073050	Chromatin interaction
ENSG00000269583	Chromatin interaction
ENSG00000167378	Chromatin interaction
ENSG00000105767	Chromatin interaction
ENSG00000226763	Chromatin interaction
ENSG00000131116	Chromatin interaction
ENSG00000159871	Chromatin interaction
ENSG00000234465	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10402946	0.85[ASW][hapmap];0.91[LWK][hapmap];0.88[YRI][hapmap]
rs17655646	0.86[CEU][hapmap]
rs2240633	1.00[CEU][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2270075	0.87[AFR][1000 genomes]
rs304719	0.85[ASW][hapmap];1.00[CEU][hapmap];0.94[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs304720	0.85[ASW][hapmap];1.00[CEU][hapmap];0.94[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs304722	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs304723	0.93[ASW][hapmap];1.00[CEU][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs304726	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs304727	0.87[ASN][1000 genomes]
rs34521657	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34637472	0.93[ASW][hapmap];1.00[CEU][hapmap];0.94[LWK][hapmap];0.94[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35346236	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs365063	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3803910	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4803646	0.82[CEU][hapmap]
rs7245651	0.91[EUR][1000 genomes]
rs8101956	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs427115	PRRG2	cis	cerebellum	SCAN
rs427115	ELSPBP1	cis	cerebellum	SCAN
rs427115	IZUMO2	cis	parietal	SCAN
rs427115	STRN4	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44079800-44098200	Weak transcription	Small Intestine	intestine
2	chr19:44084600-44098200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr19:44085600-44098800	Weak transcription	Psoas Muscle	Psoas
4	chr19:44085600-44099000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr19:44086200-44099000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr19:44086400-44098400	Weak transcription	K562	blood
7	chr19:44089000-44098200	Weak transcription	Stomach Mucosa	stomach
8	chr19:44090000-44098800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr19:44092800-44098600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr19:44093000-44098200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr19:44093000-44098200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr19:44093000-44098200	Strong transcription	Sigmoid Colon	Sigmoid Colon
13	chr19:44093000-44098200	Strong transcription	NHLF	lung
14	chr19:44093000-44098400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr19:44093000-44098400	Strong transcription	Fetal Muscle Trunk	muscle
16	chr19:44093000-44098600	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr19:44093200-44098200	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr19:44093200-44098400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr19:44094200-44098200	Strong transcription	Right Ventricle	heart
20	chr19:44094800-44098200	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr19:44094800-44098200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr19:44094800-44098400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr19:44095000-44098200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr19:44095000-44098200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr19:44095000-44098600	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr19:44095000-44098600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr19:44095000-44099000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr19:44095200-44098200	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr19:44095200-44098400	Weak transcription	HSMM	muscle
30	chr19:44095400-44098200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
31	chr19:44095400-44098400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr19:44095600-44098400	Weak transcription	Rectal Smooth Muscle	rectum
33	chr19:44096200-44098600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr19:44096200-44098800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr19:44096400-44098800	Genic enhancers	Spleen	Spleen
36	chr19:44096600-44098200	Strong transcription	Primary hematopoietic stem cells	blood
37	chr19:44096600-44098200	Genic enhancers	Pancreas	Pancrea
38	chr19:44096600-44099600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr19:44096800-44098200	Genic enhancers	Brain Cingulate Gyrus	brain
40	chr19:44096800-44098600	Genic enhancers	Brain Inferior Temporal Lobe	brain
41	chr19:44096800-44098600	Transcr. at gene 5' and 3'	Fetal Brain Female	brain
42	chr19:44096800-44098800	Genic enhancers	Primary T cells fromperipheralblood	blood
43	chr19:44096800-44098800	Transcr. at gene 5' and 3'	Brain Germinal Matrix	brain
44	chr19:44096800-44098800	Enhancers	Fetal Brain Male	brain
45	chr19:44097000-44098400	Genic enhancers	Brain Angular Gyrus	brain
46	chr19:44097000-44098600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
47	chr19:44097200-44098200	Genic enhancers	Colonic Mucosa	Colon
48	chr19:44097200-44098400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
49	chr19:44097200-44098800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr19:44097200-44098800	Genic enhancers	Placenta	Placenta

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