Variant report

Variant	rs12171099
Chromosome Location	chr22:29076637-29076638
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	JUND	chr22:29076636-29077103	HepG2	liver:	n/a	n/a
2	RXRA	chr22:29076587-29077102	HepG2	liver:	n/a	n/a
3	POLR2A	chr22:29076637-29076989	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr22:29076599-29077102	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
TTC28	TF binding region

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10084639	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10222318	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10439931	1.00[ASN][1000 genomes]
rs12165489	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12165715	0.92[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12165893	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12166245	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12166475	0.81[AFR][1000 genomes]
rs12167434	0.93[AFR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12167532	0.81[EUR][1000 genomes]
rs12167614	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12168031	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12168765	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12169071	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12169120	0.89[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12169232	0.86[AFR][1000 genomes]
rs12169262	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12169460	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12169880	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs134547	0.81[AFR][1000 genomes]
rs16986398	0.83[AFR][1000 genomes]
rs17883639	1.00[ASN][1000 genomes]
rs17883954	1.00[ASN][1000 genomes]
rs17886970	1.00[ASN][1000 genomes]
rs2013784	0.87[AFR][1000 genomes]
rs2144922	0.87[AFR][1000 genomes]
rs2881496	0.87[AFR][1000 genomes]
rs28818228	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58049055	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58542867	0.90[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6005809	0.85[AFR][1000 genomes]
rs60065194	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60248971	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60693420	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6519758	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7284670	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7288792	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7289534	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7293232	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73430118	0.90[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs73430168	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73430179	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73430189	0.92[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73432205	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8135424	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8136767	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8136905	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8136995	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8142681	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9620808	0.87[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9620809	0.86[AFR][1000 genomes]
rs9620810	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9620811	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625498	0.90[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9625509	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625512	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625513	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625514	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625516	0.86[AFR][1000 genomes]
rs9625518	0.92[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625520	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625521	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625522	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625523	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625524	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]

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:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29074600-29076800	Active TSS	Colon Smooth Muscle	Colon
2	chr22:29076200-29077400	Enhancers	Stomach Mucosa	stomach
3	chr22:29076200-29082400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr22:29076200-29089200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr22:29076200-29103000	Weak transcription	GM12878-XiMat	blood
6	chr22:29076200-29137600	Weak transcription	Esophagus	oesophagus
7	chr22:29076400-29077000	Enhancers	Pancreas	Pancrea
8	chr22:29076400-29077000	Weak transcription	Hela-S3	cervix
9	chr22:29076400-29077200	Enhancers	NHDF-Ad	bronchial
10	chr22:29076400-29077200	Enhancers	Osteobl	bone
11	chr22:29076400-29077400	Enhancers	Fetal Intestine Large	intestine
12	chr22:29076400-29077400	Enhancers	HepG2	liver
13	chr22:29076400-29082400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr22:29076400-29082400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr22:29076400-29082600	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr22:29076400-29082600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr22:29076400-29082600	Weak transcription	Spleen	Spleen
18	chr22:29076400-29084200	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr22:29076400-29085200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr22:29076400-29085400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr22:29076400-29085800	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr22:29076400-29088400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr22:29076400-29088600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr22:29076400-29092800	Weak transcription	Primary B cells from cord blood	blood
25	chr22:29076400-29098000	Weak transcription	Ovary	ovary
26	chr22:29076400-29099400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr22:29076400-29102000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr22:29076400-29103000	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr22:29076400-29105000	Weak transcription	HUVEC	blood vessel
30	chr22:29076400-29105200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr22:29076400-29105800	Weak transcription	NHLF	lung
32	chr22:29076400-29119200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr22:29076400-29129400	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr22:29076600-29077000	Enhancers	A549	lung
35	chr22:29076600-29077000	Enhancers	K562	blood
36	chr22:29076600-29077200	Weak transcription	Fetal Stomach	stomach
37	chr22:29076600-29082400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr22:29076600-29082800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr22:29076600-29083000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr22:29076600-29083000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr22:29076600-29083200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr22:29076600-29083200	Weak transcription	Fetal Muscle Leg	muscle
43	chr22:29076600-29085200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr22:29076600-29089400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr22:29076600-29094400	Weak transcription	Fetal Muscle Trunk	muscle
46	chr22:29076600-29102200	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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