Variant report

Variant	rs2713826
Chromosome Location	chr4:106341628-106341629
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:106340779..106343973-chr4:106344387..106347372,3	MCF-7	breast:

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10007134	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10020998	0.82[CEU][hapmap];0.84[CHB][hapmap];0.89[JPT][hapmap]
rs10024331	0.89[JPT][hapmap]
rs1125254	0.84[CHB][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11301777	0.87[ASN][1000 genomes]
rs1603706	0.87[ASN][1000 genomes]
rs2023840	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2046880	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]
rs2264415	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2264416	0.87[ASN][1000 genomes]
rs2264853	0.88[ASN][1000 genomes]
rs2298732	0.84[CHB][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2636693	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2636694	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2636695	0.88[ASN][1000 genomes]
rs2636727	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2636747	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2647242	0.86[ASN][1000 genomes]
rs2647252	0.88[ASN][1000 genomes]
rs2647255	0.86[ASN][1000 genomes]
rs2647265	0.84[ASN][1000 genomes]
rs2713844	0.88[ASN][1000 genomes]
rs2713845	0.87[ASN][1000 genomes]
rs2726456	0.88[ASN][1000 genomes]
rs2726496	0.88[ASN][1000 genomes]
rs2866883	0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs34248474	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35206705	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35775499	0.81[ASN][1000 genomes]
rs36112402	0.87[ASN][1000 genomes]
rs3864225	0.82[CEU][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs4235414	0.82[CEU][hapmap];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4699176	0.84[CHB][hapmap];0.89[JPT][hapmap];0.94[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4699178	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6533197	0.96[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6533198	0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6533199	0.84[CHB][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6533201	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap]
rs6816997	0.82[CEU][hapmap];0.90[JPT][hapmap]
rs72665982	0.90[EUR][1000 genomes]
rs763289	0.82[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap]
rs7678401	0.84[CHB][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs8180199	0.81[ASN][1000 genomes]
rs924282	0.86[ASN][1000 genomes]
rs924283	0.86[ASN][1000 genomes]
rs9990819	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9999896	0.84[CHB][hapmap];0.88[JPT][hapmap]

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	nsv461609	chr4:105869548-106366209	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv470063	chr4:105869548-106366209	Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv595007	chr4:105869548-106366209	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	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
5	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2713826	PPA2	cis	multi-tissue	Pritchard

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106253800-106343000	Weak transcription	Psoas Muscle	Psoas
2	chr4:106279000-106347400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr4:106280000-106344600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr4:106287600-106357000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr4:106287800-106347600	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr4:106290000-106347400	Weak transcription	Fetal Kidney	kidney
7	chr4:106290800-106345800	Weak transcription	K562	blood
8	chr4:106309400-106351000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr4:106320800-106342800	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr4:106320800-106342800	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr4:106321000-106343600	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr4:106321000-106346000	Weak transcription	Hela-S3	cervix
13	chr4:106321400-106367200	Weak transcription	HUVEC	blood vessel
14	chr4:106321600-106341800	Weak transcription	NH-A	brain
15	chr4:106321600-106356200	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr4:106321800-106353600	Weak transcription	HMEC	breast
17	chr4:106323600-106372800	Weak transcription	Stomach Mucosa	stomach
18	chr4:106324200-106347000	Weak transcription	Fetal Lung	lung
19	chr4:106326000-106356400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr4:106326000-106356600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr4:106326000-106363200	Weak transcription	Colon Smooth Muscle	Colon
22	chr4:106326200-106347600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr4:106327200-106346200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr4:106327200-106346800	Weak transcription	NHDF-Ad	bronchial
25	chr4:106327200-106365200	Weak transcription	Osteobl	bone
26	chr4:106327200-106389200	Weak transcription	Small Intestine	intestine
27	chr4:106327200-106390600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr4:106327600-106343600	Weak transcription	Primary B cells from cord blood	blood
29	chr4:106327800-106343800	Weak transcription	Primary B cells from peripheral blood	blood
30	chr4:106329000-106342800	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr4:106330400-106347200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr4:106330600-106343400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr4:106330600-106343600	Weak transcription	HSMM	muscle
34	chr4:106330600-106356400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr4:106331400-106346000	Weak transcription	Brain Substantia Nigra	brain
36	chr4:106334000-106346000	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr4:106334200-106345200	Weak transcription	Fetal Brain Female	brain
38	chr4:106334800-106347600	Weak transcription	A549	lung
39	chr4:106336400-106347600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr4:106336400-106347600	Weak transcription	NHEK	skin
41	chr4:106336600-106343000	Weak transcription	Fetal Thymus	thymus
42	chr4:106336600-106344400	Weak transcription	Brain Anterior Caudate	brain
43	chr4:106336600-106344600	Weak transcription	GM12878-XiMat	blood
44	chr4:106336600-106344800	Weak transcription	Stomach Smooth Muscle	stomach
45	chr4:106336600-106346200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr4:106336600-106347000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr4:106336600-106356400	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr4:106336800-106342800	Weak transcription	Liver	Liver
49	chr4:106336800-106343800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr4:106336800-106345000	Weak transcription	Adipose Nuclei	Adipose

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