Variant report

Variant	rs2282652
Chromosome Location	chr11:102097315-102097316
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	GATA2	chr11:102097290-102097872	HUVEC	blood vessel:	n/a	chr11:102097599-102097606 chr11:102097599-102097606 chr11:102097599-102097606 chr11:102097594-102097608
2	MAZ	chr11:102096455-102098341	IMR90	lung:	n/a	n/a
3	NFIC	chr11:102096483-102097840	SK-N-SH	brain:	n/a	n/a
4	TCF12	chr11:102097289-102097964	SK-N-SH	brain:	n/a	chr11:102097316-102097323
5	GATA3	chr11:102097256-102098001	SK-N-SH	brain:	n/a	chr11:102097599-102097606 chr11:102097599-102097606 chr11:102097599-102097606
6	GATA3	chr11:102097245-102097800	SK-N-SH	brain:	n/a	chr11:102097599-102097606 chr11:102097599-102097606 chr11:102097599-102097606
7	MYC	chr11:102096560-102097809	MCF10A-Er-Src	breast:	n/a	n/a
8	TCF12	chr11:102097279-102097999	SK-N-SH	brain:	n/a	chr11:102097316-102097323
9	JUND	chr11:102096747-102097834	Hela-S3	cervix:	n/a	chr11:102097615-102097624 chr11:102097604-102097613
10	FOS	chr11:102096481-102097809	MCF10A-Er-Src	breast:	n/a	chr11:102097613-102097624 chr11:102097615-102097624 chr11:102097604-102097613
11	MXI1	chr11:102096277-102097899	IMR90	lung:	n/a	n/a
12	POLR2A	chr11:102096833-102097713	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
YAP1	TF binding region

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10895272	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10895273	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10895274	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10895275	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10895276	1.00[CEU][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10895277	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.88[MKK][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10895278	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10895280	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10895282	0.83[ASN][1000 genomes]
rs11225156	0.95[CEU][hapmap];0.82[CHB][hapmap];0.86[EUR][1000 genomes]
rs11225160	0.91[CEU][hapmap];0.86[CHB][hapmap];0.84[EUR][1000 genomes]
rs11225163	0.90[CEU][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11225165	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11225167	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11225169	0.85[MEX][hapmap]
rs11225170	0.91[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.83[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11225174	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11225177	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11602707	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs11605954	0.91[CEU][hapmap];0.82[CHB][hapmap];0.87[GIH][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs11608234	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12223991	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12226331	0.91[CEU][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12420287	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12421242	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12786272	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12787996	0.95[CEU][hapmap];0.86[CHB][hapmap];0.87[EUR][1000 genomes]
rs12790399	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12795624	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12807220	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17097475	0.90[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs17097547	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17097560	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1820455	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1893498	0.91[CEU][hapmap];0.86[CHB][hapmap];0.87[GIH][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs2187525	0.91[CEU][hapmap];0.82[CHB][hapmap];0.87[GIH][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs2846836	0.86[MEX][hapmap]
rs3858420	1.00[CEU][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4447144	0.91[CEU][hapmap];0.82[CHB][hapmap];0.83[EUR][1000 genomes]
rs4475891	1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4754041	0.83[EUR][1000 genomes]
rs57027482	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58751289	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61280272	0.89[ASN][1000 genomes]
rs7107909	0.80[MEX][hapmap]
rs7110355	0.80[MEX][hapmap]
rs7110557	0.91[CEU][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7112802	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7120067	0.86[CEU][hapmap];0.90[CHB][hapmap];0.80[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7122907	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7124247	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs718891	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7931576	1.00[CEU][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7942061	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8504	1.00[CEU][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3362945	chr11:101736547-102114246	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 Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv1052348	chr11:101987090-102255753	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv556141	chr11:101988061-102207851	Weak transcription Genic enhancers Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1050961	chr11:101993880-102253717	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv1051735	chr11:101993880-102255753	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv530646	chr11:102000840-102238992	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
7	nsv832251	chr11:102012295-102181744	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv1043388	chr11:102017719-102172857	Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2282652	CASP1	cis	parietal	SCAN

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:102043800-102100400	Weak transcription	Pancreas	Pancrea
2	chr11:102059600-102100400	Weak transcription	Gastric	stomach
3	chr11:102064000-102105400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr11:102074000-102104200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr11:102075400-102105600	Weak transcription	Rectal Smooth Muscle	rectum
6	chr11:102076200-102102200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr11:102077000-102097400	Weak transcription	Psoas Muscle	Psoas
8	chr11:102078800-102105600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr11:102079000-102107200	Weak transcription	Fetal Brain Male	brain
10	chr11:102080800-102099600	Weak transcription	Colon Smooth Muscle	Colon
11	chr11:102081000-102100000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr11:102081200-102118600	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr11:102081400-102097800	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr11:102086800-102111600	Weak transcription	Lung	lung
15	chr11:102088600-102105200	Weak transcription	Brain Substantia Nigra	brain
16	chr11:102089200-102097800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr11:102090600-102098000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr11:102091800-102102800	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr11:102093000-102113000	Weak transcription	Ovary	ovary
20	chr11:102093400-102097600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr11:102094200-102101200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
22	chr11:102094400-102101800	Strong transcription	Liver	Liver
23	chr11:102094400-102102000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr11:102094600-102098400	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr11:102095000-102098800	Weak transcription	Fetal Kidney	kidney
26	chr11:102095200-102097600	Weak transcription	Stomach Smooth Muscle	stomach
27	chr11:102095200-102099800	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr11:102095200-102100000	Weak transcription	Duodenum Mucosa	Duodenum
29	chr11:102095200-102105400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr11:102095200-102118600	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr11:102095400-102097600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr11:102095800-102098400	Genic enhancers	HSMM	muscle
33	chr11:102095800-102099400	Strong transcription	Fetal Intestine Small	intestine
34	chr11:102095800-102101000	Strong transcription	Fetal Muscle Trunk	muscle
35	chr11:102095800-102101200	Genic enhancers	HepG2	liver
36	chr11:102096200-102097400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr11:102096200-102098200	Genic enhancers	Fetal Lung	lung
38	chr11:102096400-102097600	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr11:102096400-102097800	Enhancers	ES-I3 Cell Line	embryonic stem cell
40	chr11:102096400-102097800	Genic enhancers	A549	lung
41	chr11:102096400-102097800	Flanking Active TSS	NH-A	brain
42	chr11:102096400-102098000	Enhancers	Fetal Heart	heart
43	chr11:102096400-102098000	Enhancers	HSMMtube	muscle
44	chr11:102096400-102099600	Strong transcription	Fetal Stomach	stomach
45	chr11:102096400-102101000	Strong transcription	Fetal Muscle Leg	muscle
46	chr11:102096600-102097400	Enhancers	iPS-15b Cell Line	embryonic stem cell
47	chr11:102096600-102097800	Genic enhancers	HUES6 Cell Line	embryonic stem cell
48	chr11:102096600-102097800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr11:102096600-102097800	Genic enhancers	Left Ventricle	heart
50	chr11:102096600-102098000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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