Variant report

Variant	rs821551
Chromosome Location	chr1:155688580-155688581
allele	G/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	USF1	chr1:155688566-155688873	SK-N-SH_RA	brain:	n/a	chr1:155688717-155688728
2	USF1	chr1:155688543-155688880	K562	blood:	n/a	chr1:155688717-155688728
3	GATA2	chr1:155688423-155688792	SH-SY5Y	brain:	n/a	chr1:155688662-155688671
4	CEBPD	chr1:155688312-155688697	K562	blood:	n/a	n/a
5	USF1	chr1:155688572-155688887	K562	blood:	n/a	chr1:155688717-155688728

Variant related genes	Relation type
DAP3	TF binding region

Extended variants
information (count: 61 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10752611	0.84[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs10908470	0.84[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs10908471	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs10908479	0.91[JPT][hapmap]
rs10908481	0.90[CHB][hapmap];0.82[CHD][hapmap];0.91[JPT][hapmap]
rs10908482	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11264380	0.84[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs11264381	0.84[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs11264387	0.84[CHB][hapmap];0.83[CHD][hapmap];0.83[JPT][hapmap]
rs11264409	0.80[ASN][1000 genomes]
rs12035524	0.91[JPT][hapmap]
rs12047756	0.91[JPT][hapmap]
rs12143948	0.81[CEU][hapmap];0.84[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap]
rs12744132	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs12746592	0.84[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs1556488	0.83[CHD][hapmap];0.90[JPT][hapmap]
rs2048431	0.91[JPT][hapmap]
rs2175391	0.91[JPT][hapmap]
rs2666826	0.90[JPT][hapmap]
rs28582361	0.81[EUR][1000 genomes]
rs28662267	0.83[ASN][1000 genomes]
rs2948072	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2985707	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs348196	0.91[JPT][hapmap]
rs35615695	0.84[ASW][hapmap];0.81[CEU][hapmap];0.84[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.92[MKK][hapmap];0.81[TSI][hapmap]
rs3738590	0.91[JPT][hapmap]
rs3820594	0.84[CHB][hapmap]
rs3892792	0.84[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs4278368	0.81[ASN][1000 genomes]
rs475550	0.91[JPT][hapmap]
rs490498	1.00[ASW][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.97[MKK][hapmap]
rs490608	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6427286	0.85[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6427287	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs644853	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs6665227	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6696888	1.00[ASW][hapmap];0.81[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[MKK][hapmap];0.81[TSI][hapmap]
rs670523	1.00[ASW][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.97[MKK][hapmap]
rs678157	0.91[JPT][hapmap]
rs708611	0.96[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs729022	0.85[CEU][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs7541060	0.96[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7550402	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs822025	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs822478	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap]
rs822490	0.92[CEU][hapmap];0.84[CHB][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap]
rs822505	0.84[CEU][hapmap]
rs822508	0.85[CEU][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap]
rs822527	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs860295	0.92[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap]
rs9426933	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529709	chr1:155154933-155757219	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	450 gene(s)	inside rSNPs	diseases
2	esv33869	chr1:155223283-155917961	Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	nsv1002390	chr1:155553423-155706930	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv428246	chr1:155558197-155785831	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv547965	chr1:155563152-155688600	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
6	esv3381327	chr1:155582853-155718436	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
7	esv3436971	chr1:155618172-155733386	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
8	esv3338099	chr1:155618190-155733359	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
9	esv3423892	chr1:155664084-155901487	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
10	nsv3065	chr1:155682768-155727524	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs821551	THEM5	cis	parietal	SCAN
rs821551	RIT1	cis	cerebellum	SCAN
rs821551	ADAM15	cis	multi-tissue	Pritchard
rs821551	ROBLD3	cis	parietal	SCAN
rs821551	SPRR3	cis	parietal	SCAN
rs821551	YY1AP1	cis	cerebellum	SCAN
rs821551	PRUNE	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155660200-155698800	Weak transcription	NHLF	lung
2	chr1:155660400-155688800	Weak transcription	Lung	lung
3	chr1:155660400-155706200	Weak transcription	Colonic Mucosa	Colon
4	chr1:155661600-155688600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr1:155661600-155707800	Weak transcription	HUVEC	blood vessel
6	chr1:155663200-155701000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr1:155665200-155708000	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr1:155665400-155695000	Weak transcription	Pancreas	Pancrea
9	chr1:155665400-155699000	Weak transcription	Right Ventricle	heart
10	chr1:155665600-155707200	Weak transcription	Psoas Muscle	Psoas
11	chr1:155665800-155707000	Weak transcription	Small Intestine	intestine
12	chr1:155667600-155689600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr1:155669200-155702200	Weak transcription	Gastric	stomach
14	chr1:155672800-155698800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr1:155673200-155695000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr1:155673800-155707800	Weak transcription	Aorta	Aorta
17	chr1:155676000-155695000	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr1:155676400-155689400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr1:155676400-155691800	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr1:155676400-155695400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr1:155676400-155698600	Weak transcription	Stomach Mucosa	stomach
22	chr1:155676400-155706200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr1:155677200-155691400	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr1:155677400-155705200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:155678800-155689000	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr1:155679200-155688600	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr1:155679200-155688800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr1:155679200-155689600	Weak transcription	Thymus	Thymus
29	chr1:155679200-155691800	Weak transcription	Ovary	ovary
30	chr1:155679400-155710400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr1:155679800-155688600	Weak transcription	Fetal Lung	lung
32	chr1:155679800-155695200	Weak transcription	Fetal Brain Female	brain
33	chr1:155679800-155704200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr1:155681600-155696800	Weak transcription	Rectal Smooth Muscle	rectum
35	chr1:155681600-155707800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr1:155681800-155688800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr1:155681800-155689800	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr1:155681800-155690200	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr1:155681800-155693600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr1:155682000-155690200	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr1:155682200-155692000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr1:155682400-155690600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr1:155682600-155688600	Weak transcription	Fetal Intestine Small	intestine
44	chr1:155682600-155690400	Strong transcription	Placenta	Placenta
45	chr1:155682800-155697200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr1:155683000-155688800	Weak transcription	Brain Substantia Nigra	brain
47	chr1:155683000-155691200	Weak transcription	HSMMtube	muscle
48	chr1:155683000-155703200	Weak transcription	Spleen	Spleen
49	chr1:155683200-155695200	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr1:155683200-155715000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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