Variant report

Variant	rs12169262
Chromosome Location	chr22:29079353-29079354
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	USF1	chr22:29079220-29079405	H1-hESC	embryonic stem cell:	n/a	n/a
2	FOSL2	chr22:29079346-29079699	HepG2	liver:	n/a	chr22:29079630-29079639
3	USF1	chr22:29079224-29079551	HepG2	liver:	n/a	n/a
4	ZBTB33	chr22:29079307-29079689	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
TTC28	TF binding region

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10084639	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10222318	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10439931	1.00[ASN][1000 genomes]
rs12165489	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12165715	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs12165893	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12166245	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12166716	1.00[CHB][hapmap]
rs12167434	1.00[ASN][1000 genomes]
rs12167614	1.00[ASN][1000 genomes]
rs12168031	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12168765	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12169071	1.00[ASN][1000 genomes]
rs12169120	1.00[ASN][1000 genomes]
rs12169460	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12169880	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12171099	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13057011	1.00[CHB][hapmap]
rs1474961	0.83[CEU][hapmap]
rs16986509	0.91[CEU][hapmap];0.95[YRI][hapmap]
rs17507066	0.83[CEU][hapmap]
rs17883639	1.00[ASN][1000 genomes]
rs17883954	1.00[ASN][1000 genomes]
rs17886970	1.00[ASN][1000 genomes]
rs2013784	1.00[CEU][hapmap]
rs2144922	1.00[CEU][hapmap]
rs28818228	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58049055	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58542867	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6005807	0.91[CEU][hapmap];0.96[YRI][hapmap]
rs60065194	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60248971	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60693420	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6519758	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7284670	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7288792	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7289534	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7289625	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs7291268	0.91[CEU][hapmap];0.96[YRI][hapmap]
rs7293232	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73430168	0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73430179	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73430189	1.00[ASN][1000 genomes]
rs73432205	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8135424	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8136767	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8136905	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8136995	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8142681	1.00[ASN][1000 genomes]
rs9306457	0.91[CEU][hapmap];0.96[YRI][hapmap]
rs9608696	1.00[CEU][hapmap]
rs9620797	0.91[CEU][hapmap];0.95[YRI][hapmap]
rs9620799	0.96[YRI][hapmap]
rs9620804	0.91[CEU][hapmap];0.96[YRI][hapmap]
rs9620808	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs9620810	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9620811	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9620826	1.00[CHB][hapmap]
rs9620828	1.00[CHB][hapmap]
rs9625498	0.81[EUR][1000 genomes]
rs9625509	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625512	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625513	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625514	0.92[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625518	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625520	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625521	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625522	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625523	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625524	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625534	0.83[CEU][hapmap]
rs9625554	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916473	chr22:28837041-29215603	Weak transcription Bivalent Enhancer Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
2	nsv459867	chr22:28993183-29109036	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv588881	chr22:28993183-29109036	Weak transcription Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1061684	chr22:29026341-29088590	Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv9895	chr22:29029961-29184277	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS 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	25 gene(s)	inside rSNPs	diseases
6	nsv1064624	chr22:29065528-29130728	Active TSS Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1064079	chr22:29065528-29456059	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
8	esv17527	chr22:29066121-29102976	Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv966098	chr22:29069640-29088208	Weak transcription Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv966097	chr22:29069640-29092062	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	esv1832949	chr22:29072426-29092190	Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	esv1806615	chr22:29072426-29095085	Bivalent/Poised TSS Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	esv1828355	chr22:29072426-29095085	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	esv1843637	chr22:29072426-29095085	Strong transcription Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
15	esv1832454	chr22:29074021-29094885	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29076200-29082400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr22:29076200-29089200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr22:29076200-29103000	Weak transcription	GM12878-XiMat	blood
4	chr22:29076200-29137600	Weak transcription	Esophagus	oesophagus
5	chr22:29076400-29082400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr22:29076400-29082400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr22:29076400-29082600	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr22:29076400-29082600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr22:29076400-29082600	Weak transcription	Spleen	Spleen
10	chr22:29076400-29084200	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr22:29076400-29085200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr22:29076400-29085400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr22:29076400-29085800	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr22:29076400-29088400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr22:29076400-29088600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr22:29076400-29092800	Weak transcription	Primary B cells from cord blood	blood
17	chr22:29076400-29098000	Weak transcription	Ovary	ovary
18	chr22:29076400-29099400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr22:29076400-29102000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr22:29076400-29103000	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr22:29076400-29105000	Weak transcription	HUVEC	blood vessel
22	chr22:29076400-29105200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr22:29076400-29105800	Weak transcription	NHLF	lung
24	chr22:29076400-29119200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr22:29076400-29129400	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr22:29076600-29082400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr22:29076600-29082800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr22:29076600-29083000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr22:29076600-29083000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr22:29076600-29083200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr22:29076600-29083200	Weak transcription	Fetal Muscle Leg	muscle
32	chr22:29076600-29085200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr22:29076600-29089400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr22:29076600-29094400	Weak transcription	Fetal Muscle Trunk	muscle
35	chr22:29076600-29102200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr22:29077200-29105000	Weak transcription	Osteobl	bone
37	chr22:29077400-29082200	Weak transcription	Fetal Stomach	stomach
38	chr22:29077400-29102000	Weak transcription	Fetal Intestine Large	intestine
39	chr22:29077400-29106000	Weak transcription	A549	lung
40	chr22:29077600-29099000	Weak transcription	Hela-S3	cervix
41	chr22:29077600-29102800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr22:29078400-29082600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr22:29079000-29089200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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