Variant report

Variant	rs11097889
Chromosome Location	chr4:106367696-106367697
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:106365210..106367953-chr4:106377715..106379530,2	MCF-7	breast:
2	chr4:106367022..106369880-chr4:106393183..106396480,3	K562	blood:
3	chr4:106366716..106368636-chr4:106386023..106388059,2	K562	blood:

Variant related genes	Relation type
ENSG00000138777	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs11097890	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs11737582	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12108243	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs12108480	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12108594	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17035483	1.00[AMR][1000 genomes]
rs17035566	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17035569	0.85[AFR][1000 genomes]
rs17035594	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17035595	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17035596	1.00[YRI][hapmap]
rs17035600	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17035605	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17035609	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17035618	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28417349	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs41485844	1.00[ASW][hapmap];0.84[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs41505250	1.00[ASW][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57620916	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57624740	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60734979	1.00[AMR][1000 genomes]
rs72950516	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72950533	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72950537	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72950550	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72950555	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72950565	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72950576	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72950590	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72950594	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72950598	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72950601	0.80[AFR][1000 genomes]
rs72952256	0.80[AFR][1000 genomes]
rs72952259	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72952274	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72952276	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72952281	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72952296	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72952301	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72952362	1.00[AMR][1000 genomes]
rs72952393	1.00[AMR][1000 genomes]
rs72962224	1.00[AMR][1000 genomes]
rs72962234	1.00[AMR][1000 genomes]
rs72962246	1.00[AMR][1000 genomes]
rs72962257	1.00[AMR][1000 genomes]
rs72962270	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72962273	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72963039	1.00[AMR][1000 genomes]
rs72964211	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72964213	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72964224	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72964228	0.83[AFR][1000 genomes]
rs72964242	0.85[AFR][1000 genomes]
rs72964244	0.85[AFR][1000 genomes]
rs72964262	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72964265	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72964271	0.85[AFR][1000 genomes]
rs72964288	0.85[AFR][1000 genomes]
rs7695564	1.00[AMR][1000 genomes]
rs9968337	0.87[YRI][hapmap];0.85[AFR][1000 genomes]
rs9968402	0.85[AFR][1000 genomes]
rs9968408	1.00[AMR][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
rs11097889	PPA2	cis	lymphoblastoid	seeQTL

Chromatin state (count:115 , 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	chr4:106346600-106369000	Weak transcription	Hela-S3	cervix
9	chr4:106347600-106392800	Weak transcription	Colonic Mucosa	Colon
10	chr4:106347800-106375200	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr4:106348000-106375000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr4:106348000-106376400	Weak transcription	Gastric	stomach
13	chr4:106348000-106376800	Weak transcription	Pancreas	Pancrea
14	chr4:106348000-106388000	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr4:106348200-106387800	Weak transcription	Lung	lung
16	chr4:106348200-106393000	Weak transcription	Thymus	Thymus
17	chr4:106348400-106384200	Weak transcription	Fetal Stomach	stomach
18	chr4:106348600-106384600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr4:106348800-106375000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr4:106352200-106375000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr4:106355400-106378800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr4:106355400-106393200	Weak transcription	Esophagus	oesophagus
23	chr4:106356800-106372600	Weak transcription	NH-A	brain
24	chr4:106357000-106372800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr4:106357200-106374200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr4:106357200-106381000	Weak transcription	Brain Cingulate Gyrus	brain
27	chr4:106357200-106381000	Weak transcription	Brain Substantia Nigra	brain
28	chr4:106357200-106387600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr4:106357200-106392600	Weak transcription	Brain Angular Gyrus	brain
30	chr4:106357600-106392200	Weak transcription	Rectal Smooth Muscle	rectum
31	chr4:106357800-106371400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr4:106358000-106369200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr4:106358200-106369600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr4:106358600-106370200	Weak transcription	K562	blood
35	chr4:106358800-106372600	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr4:106359000-106373000	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr4:106359000-106378800	Weak transcription	Fetal Intestine Small	intestine
38	chr4:106359000-106382400	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr4:106359000-106387600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr4:106359200-106382200	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr4:106359600-106379800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr4:106360000-106373400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr4:106361000-106369200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr4:106361000-106369600	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr4:106361200-106368200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr4:106361200-106368600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr4:106361200-106378000	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr4:106361400-106379600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr4:106361600-106367800	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr4:106361600-106368200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood

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