Variant report

Variant	rs17035553
Chromosome Location	chr4:106321423-106321424
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFIC	chr4:106320673-106321455	SK-N-SH	brain:	n/a	n/a
2	EP300	chr4:106320692-106321545	SK-N-SH	brain:	n/a	chr4:106321367-106321377
3	JUND	chr4:106320732-106321489	SK-N-SH	brain:	n/a	n/a
4	EP300	chr4:106320762-106321541	SK-N-SH	brain:	n/a	chr4:106321367-106321377
5	PBX3	chr4:106320776-106321481	SK-N-SH	brain:	n/a	n/a
6	TCF12	chr4:106320716-106321543	SK-N-SH	brain:	n/a	n/a
7	TEAD4	chr4:106320866-106321487	SK-N-SH	brain:	n/a	n/a
8	TCF12	chr4:106320700-106321526	SK-N-SH	brain:	n/a	n/a
9	GATA3	chr4:106320652-106321525	SK-N-SH	brain:	n/a	n/a
10	GATA3	chr4:106320548-106321698	SK-N-SH	brain:	n/a	n/a
11	JUND	chr4:106320800-106321488	SK-N-SH	brain:	n/a	n/a
12	GATA1	chr4:106320987-106321473	PBDE	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:106319989..106322033-chr4:106394167..106395857,2	K562	blood:

Variant related genes	Relation type
PPA2	TF binding region
ENSG00000138777	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1017988	1.00[ASN][1000 genomes]
rs1077526	1.00[CEU][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1126066	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17035461	0.85[EUR][1000 genomes]
rs17035550	1.00[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17035551	1.00[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17035557	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17035558	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17035568	1.00[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17035581	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17035584	1.00[ASN][1000 genomes]
rs17035586	1.00[ASN][1000 genomes]
rs17035619	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17509136	1.00[ASN][1000 genomes]
rs1874758	0.82[CEU][hapmap]
rs2004290	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3898404	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4499701	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4519798	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55652556	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55755102	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55874621	1.00[ASN][1000 genomes]
rs56397029	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59902936	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62317353	1.00[ASN][1000 genomes]
rs6533194	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66517713	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66763438	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66932244	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66956902	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66988826	1.00[ASN][1000 genomes]
rs67248885	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67476913	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67554145	1.00[ASN][1000 genomes]
rs6811159	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6829168	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6856615	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6857688	0.86[EUR][1000 genomes]
rs72668208	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72668215	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72668219	1.00[ASN][1000 genomes]
rs72668239	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]

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
rs17035553	PPA2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:104 , 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	chr4:106274400-106326800	Weak transcription	Small Intestine	intestine
3	chr4:106274800-106330400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr4:106279000-106339600	Weak transcription	HSMMtube	muscle
5	chr4:106279000-106347400	Weak transcription	Rectal Smooth Muscle	rectum
6	chr4:106280000-106344600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr4:106281000-106326800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr4:106282600-106325800	Weak transcription	Brain Angular Gyrus	brain
9	chr4:106282600-106335600	Weak transcription	Brain Cingulate Gyrus	brain
10	chr4:106283600-106330000	Weak transcription	Right Ventricle	heart
11	chr4:106285000-106326000	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr4:106287000-106335800	Weak transcription	Colonic Mucosa	Colon
13	chr4:106287600-106335600	Weak transcription	Esophagus	oesophagus
14	chr4:106287600-106357000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr4:106287800-106326800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr4:106287800-106330200	Weak transcription	Gastric	stomach
17	chr4:106287800-106335400	Weak transcription	Spleen	Spleen
18	chr4:106287800-106335800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr4:106287800-106347600	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr4:106288400-106330200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr4:106288400-106330200	Weak transcription	Lung	lung
22	chr4:106288600-106325600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr4:106288600-106335400	Weak transcription	Thymus	Thymus
24	chr4:106288800-106325600	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr4:106289200-106325600	Weak transcription	Fetal Muscle Leg	muscle
26	chr4:106289600-106335400	Weak transcription	Brain Anterior Caudate	brain
27	chr4:106290000-106347400	Weak transcription	Fetal Kidney	kidney
28	chr4:106290800-106325600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr4:106290800-106345800	Weak transcription	K562	blood
30	chr4:106293400-106330200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr4:106304200-106326800	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr4:106304400-106330400	Weak transcription	Fetal Stomach	stomach
33	chr4:106304400-106335600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr4:106305000-106325800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr4:106305400-106325800	Weak transcription	Fetal Intestine Small	intestine
36	chr4:106306400-106325600	Weak transcription	Colon Smooth Muscle	Colon
37	chr4:106306400-106325800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr4:106306400-106335200	Weak transcription	Placenta	Placenta
39	chr4:106306400-106335400	Weak transcription	Fetal Muscle Trunk	muscle
40	chr4:106306400-106335400	Weak transcription	Stomach Smooth Muscle	stomach
41	chr4:106306800-106326600	Weak transcription	Dnd41	blood
42	chr4:106308400-106335800	Weak transcription	Brain Hippocampus Middle	brain
43	chr4:106308800-106326800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr4:106309000-106325800	Weak transcription	Fetal Thymus	thymus
45	chr4:106309400-106325600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr4:106309400-106351000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr4:106312400-106335600	Weak transcription	Ovary	ovary
48	chr4:106313000-106326400	Weak transcription	Primary T cells from cord blood	blood
49	chr4:106314600-106326800	Weak transcription	Duodenum Mucosa	Duodenum
50	chr4:106314600-106335600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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