Variant report

Variant	rs2046880
Chromosome Location	chr4:106370816-106370817
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:106368296..106371376-chr4:106372704..106375922,3	K562	blood:

Variant related genes	Relation type
ENSG00000138777	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10007134	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10020998	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10024331	1.00[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap]
rs1125254	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11934602	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11934709	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2023840	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2298732	0.91[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2636693	0.82[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap]
rs2636694	0.87[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap]
rs2636727	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2636747	0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2713826	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2866883	0.86[CHB][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs34248474	0.82[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap]
rs35775499	0.90[ASN][1000 genomes]
rs3864225	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs4235414	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4699176	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4699178	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6533196	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6533197	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6533198	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6533199	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6533201	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6816997	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6836448	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs763289	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7678401	0.91[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7691192	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8180199	0.90[ASN][1000 genomes]
rs981136	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9990819	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9999896	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879699	chr4:106212562-106698892	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv830027	chr4:106222010-106406738	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv1002228	chr4:106346206-106433381	ZNF genes & repeats Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	esv2760858	chr4:106351454-106376197	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2046880	PPA2	cis	multi-tissue	Pritchard

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106323600-106372800	Weak transcription	Stomach Mucosa	stomach
2	chr4:106327200-106389200	Weak transcription	Small Intestine	intestine
3	chr4:106327200-106390600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr4:106336800-106376400	Weak transcription	Right Ventricle	heart
5	chr4:106336800-106387800	Weak transcription	NHLF	lung
6	chr4:106340200-106387800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr4:106341600-106376000	Weak transcription	Fetal Heart	heart
8	chr4:106347600-106392800	Weak transcription	Colonic Mucosa	Colon
9	chr4:106347800-106375200	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr4:106348000-106375000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr4:106348000-106376400	Weak transcription	Gastric	stomach
12	chr4:106348000-106376800	Weak transcription	Pancreas	Pancrea
13	chr4:106348000-106388000	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr4:106348200-106387800	Weak transcription	Lung	lung
15	chr4:106348200-106393000	Weak transcription	Thymus	Thymus
16	chr4:106348400-106384200	Weak transcription	Fetal Stomach	stomach
17	chr4:106348600-106384600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr4:106348800-106375000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr4:106352200-106375000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr4:106355400-106378800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr4:106355400-106393200	Weak transcription	Esophagus	oesophagus
22	chr4:106356800-106372600	Weak transcription	NH-A	brain
23	chr4:106357000-106372800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr4:106357200-106374200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr4:106357200-106381000	Weak transcription	Brain Cingulate Gyrus	brain
26	chr4:106357200-106381000	Weak transcription	Brain Substantia Nigra	brain
27	chr4:106357200-106387600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr4:106357200-106392600	Weak transcription	Brain Angular Gyrus	brain
29	chr4:106357600-106392200	Weak transcription	Rectal Smooth Muscle	rectum
30	chr4:106357800-106371400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr4:106358800-106372600	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr4:106359000-106373000	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr4:106359000-106378800	Weak transcription	Fetal Intestine Small	intestine
34	chr4:106359000-106382400	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr4:106359000-106387600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr4:106359200-106382200	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr4:106359600-106379800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr4:106360000-106373400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr4:106361200-106378000	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr4:106361400-106379600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr4:106361800-106387800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr4:106362200-106392600	Weak transcription	A549	lung
43	chr4:106362400-106379000	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr4:106363400-106377600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr4:106363800-106390200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr4:106364000-106378000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr4:106364200-106372600	Weak transcription	Primary B cells from cord blood	blood
48	chr4:106364200-106373400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr4:106364400-106384200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr4:106364600-106372600	Weak transcription	Colon Smooth Muscle	Colon

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