Variant report

Variant	rs3803453
Chromosome Location	chr15:57538108-57538109
allele	A/G
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	TEAD4	chr15:57537964-57538269	K562	blood:	n/a	n/a
2	EP300	chr15:57538086-57538227	K562	blood:	n/a	n/a
3	TAL1	chr15:57537952-57538311	K562	blood:	n/a	chr15:57538302-57538310
4	RCOR1	chr15:57537993-57538231	K562	blood:	n/a	n/a
5	TEAD4	chr15:57537917-57538301	K562	blood:	n/a	n/a
6	RCOR1	chr15:57537652-57538297	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:57519601..57521233-chr15:57537567..57539134,2	K562	blood:

Variant related genes	Relation type
TCF12	TF binding region

Extended variants
information (count: 60 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10467927	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs10467928	0.91[JPT][hapmap]
rs10467929	0.91[JPT][hapmap]
rs11071308	0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap]
rs11853810	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11856210	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11856411	0.85[JPT][hapmap]
rs13379847	0.90[JPT][hapmap]
rs16977243	0.90[GIH][hapmap]
rs16977270	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs16977278	0.95[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.84[TSI][hapmap];0.81[ASN][1000 genomes]
rs16977374	0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.86[TSI][hapmap];0.91[ASN][1000 genomes]
rs2169467	0.91[JPT][hapmap]
rs2414493	0.85[JPT][hapmap]
rs2593211	0.95[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.84[TSI][hapmap]
rs2593249	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2593252	0.89[JPT][hapmap]
rs2615226	0.92[ASN][1000 genomes]
rs2615227	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2703593	0.81[TSI][hapmap]
rs2703595	0.81[TSI][hapmap]
rs2703614	0.90[GIH][hapmap];0.91[JPT][hapmap]
rs2733323	0.94[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.91[TSI][hapmap];0.88[ASN][1000 genomes]
rs2733333	0.87[GIH][hapmap];0.91[JPT][hapmap]
rs2733334	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs28445470	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28653088	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4774915	1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4774916	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55742030	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6493900	0.91[JPT][hapmap]
rs6493907	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7163267	0.91[JPT][hapmap]
rs7164298	0.89[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.94[MKK][hapmap];0.94[TSI][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7164914	0.95[ASN][1000 genomes]
rs7171073	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs7173477	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7173748	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7176873	0.90[JPT][hapmap]
rs7179311	0.81[CEU][hapmap]
rs7180558	0.87[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.89[TSI][hapmap];0.92[ASN][1000 genomes]
rs7181399	0.81[EUR][1000 genomes]
rs720290	0.81[JPT][hapmap]
rs8024901	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.92[ASN][1000 genomes]
rs8026702	0.84[ASW][hapmap];0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.84[ASN][1000 genomes]
rs8034502	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs8034744	0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs8034843	0.94[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.88[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8035916	0.89[JPT][hapmap]
rs8037956	0.86[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs8039176	0.85[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs9672676	0.82[CEU][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap]
rs9806170	0.82[GIH][hapmap];0.81[JPT][hapmap]
rs9806199	0.91[JPT][hapmap]
rs997683	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[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	nsv904251	chr15:57241970-57575916	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1045611	chr15:57350965-58070807	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv457164	chr15:57495060-57559387	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv569578	chr15:57495060-57559387	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv833021	chr15:57495413-57751366	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3803453	AQP9	cis	cerebellum	SCAN
rs3803453	TCF12	Cis_1M	lymphoblastoid	RTeQTL
rs3803453	DHX9	trans	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57511800-57551600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:57511800-57565000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr15:57519600-57544600	Weak transcription	Psoas Muscle	Psoas
4	chr15:57520400-57576000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr15:57520800-57544600	Weak transcription	Colon Smooth Muscle	Colon
6	chr15:57522400-57565400	Weak transcription	Spleen	Spleen
7	chr15:57522800-57585000	Strong transcription	Fetal Thymus	thymus
8	chr15:57524400-57540600	Strong transcription	Primary T cells from cord blood	blood
9	chr15:57525600-57556800	Weak transcription	Pancreas	Pancrea
10	chr15:57526000-57539000	Weak transcription	Gastric	stomach
11	chr15:57526000-57539200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr15:57526000-57539200	Weak transcription	Lung	lung
13	chr15:57526000-57542600	Weak transcription	Right Ventricle	heart
14	chr15:57526000-57550200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr15:57526400-57539200	Weak transcription	Aorta	Aorta
16	chr15:57526600-57539000	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr15:57526600-57545400	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr15:57526600-57554400	Weak transcription	Rectal Smooth Muscle	rectum
19	chr15:57526600-57574200	Weak transcription	Hela-S3	cervix
20	chr15:57526800-57545400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr15:57526800-57554200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr15:57527200-57538200	Weak transcription	Stomach Smooth Muscle	stomach
23	chr15:57528200-57545200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr15:57528400-57538600	Weak transcription	Ovary	ovary
25	chr15:57528400-57545400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr15:57528400-57554800	Weak transcription	NHEK	skin
27	chr15:57528600-57539000	Weak transcription	A549	lung
28	chr15:57529000-57538600	Weak transcription	Placenta	Placenta
29	chr15:57529000-57545400	Weak transcription	HMEC	breast
30	chr15:57529400-57543400	Weak transcription	HUVEC	blood vessel
31	chr15:57529600-57540000	Weak transcription	Fetal Heart	heart
32	chr15:57529800-57538600	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr15:57530200-57543400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr15:57530800-57551200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr15:57531000-57542400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr15:57531400-57541200	Strong transcription	Fetal Muscle Trunk	muscle
37	chr15:57531600-57540200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr15:57533600-57568800	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr15:57535000-57539600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr15:57535000-57540000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr15:57535000-57541200	Strong transcription	NH-A	brain
42	chr15:57535200-57540000	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr15:57535200-57542600	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr15:57535400-57540000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr15:57535400-57540000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr15:57535600-57539600	Strong transcription	HUES6 Cell Line	embryonic stem cell
47	chr15:57535600-57539600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr15:57535600-57539800	Strong transcription	Adipose Nuclei	Adipose
49	chr15:57535600-57540200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
50	chr15:57535600-57540200	Strong transcription	Primary B cells from peripheral blood	blood

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