Variant report

Variant	rs138642
Chromosome Location	chr22:28387749-28387750
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	ELF1	chr22:28387534-28388257	GM12878	blood:	n/a	n/a
2	RUNX3	chr22:28387732-28388248	GM12878	blood:	n/a	n/a
3	ZNF263	chr22:28386793-28387877	HEK293-T-REx	kidney:	n/a	n/a
4	TCF3	chr22:28387705-28388130	GM12878	blood:	n/a	chr22:28387976-28387990 chr22:28387979-28387988 chr22:28387976-28387991
5	ZNF143	chr22:28387694-28387757	GM12878	blood:	n/a	n/a
6	RUNX3	chr22:28387745-28388217	GM12878	blood:	n/a	n/a
7	PAX5	chr22:28387653-28388112	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr22:28386557..28389416-chr22:28392270..28394268,2	MCF-7	breast:
2	chr22:28387405..28389960-chr22:28390673..28392531,2	K562	blood:
3	chr22:28386424..28391096-chr22:28391178..28396307,7	MCF-7	breast:
4	chr22:28314687..28317374-chr22:28386537..28389209,3	MCF-7	breast:

Variant related genes	Relation type
TTC28-AS1	TF binding region
TTC28	TF binding region
ENSG00000235954	Chromatin interaction
ENSG00000180957	Chromatin interaction
ENSG00000100154	Chromatin interaction
ENSG00000264073	Chromatin interaction

Extended variants
information (count: 162 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:160)

rs_ID	r²[population]
rs10154425	0.89[CEU][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10212007	0.86[AMR][1000 genomes]
rs10212036	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10212040	0.81[AMR][1000 genomes]
rs10212074	0.82[AMR][1000 genomes]
rs10483140	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10483142	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10483143	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs118840	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12165651	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12165797	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12166023	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12166077	1.00[ASW][hapmap];0.89[CEU][hapmap];0.87[TSI][hapmap];0.83[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs12166158	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12166164	0.81[EUR][1000 genomes]
rs12166256	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12166389	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12166719	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12166740	0.87[TSI][hapmap];0.93[EUR][1000 genomes]
rs12166912	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12166938	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12167320	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12167735	0.83[AMR][1000 genomes]
rs12167829	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12168054	0.89[CEU][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12168180	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12168251	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12168582	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12168652	0.83[AMR][1000 genomes]
rs12169097	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12169888	0.95[EUR][1000 genomes]
rs12169936	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12170022	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12170558	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12170953	0.89[CEU][hapmap];0.95[EUR][1000 genomes]
rs12171104	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs134197	0.80[AMR][1000 genomes]
rs138636	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs138637	1.00[CEU][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs138639	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs138640	1.00[CEU][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs138646	0.81[CEU][hapmap];0.89[MEX][hapmap]
rs138651	0.86[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs138653	0.89[CEU][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs138654	0.89[CEU][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs138655	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs138656	0.89[CEU][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs138658	0.89[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs138660	0.89[CEU][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs138664	0.89[CEU][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs138665	0.89[CEU][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs138667	0.89[CEU][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs138669	0.87[EUR][1000 genomes]
rs138670	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs138671	0.89[CEU][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs138672	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16985763	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16985967	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs16985976	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs16986037	0.88[MEX][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16986077	0.88[MEX][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs16987005	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17390800	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17407024	0.88[CEU][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17483887	0.89[CEU][hapmap];0.87[TSI][hapmap];0.95[EUR][1000 genomes]
rs17484337	0.89[CEU][hapmap];0.95[EUR][1000 genomes]
rs17487463	0.80[AMR][1000 genomes]
rs2745562	0.86[CEU][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28375646	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28579300	0.83[AMR][1000 genomes]
rs4036493	0.83[AMR][1000 genomes]
rs470098	1.00[CEU][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs470101	0.90[CEU][hapmap];0.89[MEX][hapmap]
rs470102	0.89[CEU][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs470103	0.89[CEU][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs470104	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55856549	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56233401	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56393679	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs57686964	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs58050941	0.89[EUR][1000 genomes]
rs58823697	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7286519	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7288331	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7289984	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7292562	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73880355	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73880374	0.95[EUR][1000 genomes]
rs73880375	0.95[EUR][1000 genomes]
rs73880376	0.95[EUR][1000 genomes]
rs73880381	0.95[EUR][1000 genomes]
rs73880382	0.87[EUR][1000 genomes]
rs73880383	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73880384	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73880385	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73880387	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73880393	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73880395	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73882704	0.83[AMR][1000 genomes]
rs73882705	0.83[AMR][1000 genomes]
rs761322	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs761323	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8141163	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8141173	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9306451	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9306452	0.88[MEX][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9620752	0.81[CEU][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9620753	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9620755	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9620757	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9620762	0.89[CEU][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9620764	0.89[CEU][hapmap];0.87[TSI][hapmap];0.95[EUR][1000 genomes]
rs9620766	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9620767	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9620768	0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9620769	0.88[MEX][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9620770	0.88[MEX][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9620771	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9620778	0.80[AMR][1000 genomes]
rs9625352	0.89[MEX][hapmap]
rs9625361	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9625363	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9625366	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9625367	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9625370	0.98[EUR][1000 genomes]
rs9625374	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9625375	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9625377	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9625387	0.89[CEU][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9625388	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9625390	0.89[CEU][hapmap];0.95[EUR][1000 genomes]
rs9625391	0.89[CEU][hapmap];0.87[TSI][hapmap];0.93[EUR][1000 genomes]
rs9625393	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9625395	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9625396	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9625397	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9625398	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9625399	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9625400	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9625402	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9625403	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9625405	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9625406	0.80[EUR][1000 genomes]
rs9625408	0.89[CEU][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9625409	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9625410	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9625413	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9625415	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9625416	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9625417	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9625418	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9625421	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9625425	0.83[AMR][1000 genomes]
rs9625427	0.83[AMR][1000 genomes]
rs9625430	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9625433	0.83[AMR][1000 genomes]
rs9625440	0.80[AMR][1000 genomes]
rs9712839	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs988893	0.80[AMR][1000 genomes]
rs9985213	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062877	chr22:28163507-28866350	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv522306	chr22:28378472-28402624	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28355400-28387800	Weak transcription	Fetal Brain Male	brain
2	chr22:28360800-28392400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr22:28369200-28398400	Weak transcription	Hela-S3	cervix
4	chr22:28369400-28394000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr22:28371800-28395000	Weak transcription	Small Intestine	intestine
6	chr22:28373600-28404000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr22:28373800-28398200	Strong transcription	Fetal Brain Female	brain
8	chr22:28373800-28404200	Strong transcription	Fetal Stomach	stomach
9	chr22:28373800-28405200	Strong transcription	Fetal Intestine Small	intestine
10	chr22:28377200-28388600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr22:28377800-28391800	Strong transcription	Fetal Lung	lung
12	chr22:28377800-28398000	Strong transcription	Fetal Intestine Large	intestine
13	chr22:28377800-28398600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr22:28378000-28396600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr22:28379400-28399600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr22:28379800-28388200	Weak transcription	Colonic Mucosa	Colon
17	chr22:28380200-28390400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr22:28381000-28388200	Weak transcription	Esophagus	oesophagus
19	chr22:28381400-28388200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr22:28381600-28393800	Weak transcription	Duodenum Mucosa	Duodenum
21	chr22:28381800-28412400	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr22:28382000-28388800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr22:28382200-28394000	Weak transcription	Brain Substantia Nigra	brain
24	chr22:28382800-28391800	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr22:28382800-28394600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr22:28383200-28388200	Weak transcription	Gastric	stomach
27	chr22:28383600-28388000	Weak transcription	Rectal Smooth Muscle	rectum
28	chr22:28384000-28390600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr22:28384000-28405000	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr22:28384200-28387800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr22:28384200-28390600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr22:28384200-28399400	Weak transcription	Primary hematopoietic stem cells	blood
33	chr22:28384400-28392600	Strong transcription	Brain Germinal Matrix	brain
34	chr22:28384600-28397600	Strong transcription	Ovary	ovary
35	chr22:28384800-28401600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr22:28385000-28388000	Weak transcription	HSMMtube	muscle
37	chr22:28385000-28390400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr22:28385000-28393400	Weak transcription	HSMM	muscle
39	chr22:28385200-28387800	Weak transcription	Pancreas	Pancrea
40	chr22:28385200-28390800	Weak transcription	Brain Hippocampus Middle	brain
41	chr22:28386000-28387800	Genic enhancers	Placenta	Placenta
42	chr22:28386000-28388400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr22:28386000-28389200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
44	chr22:28386000-28390000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr22:28386200-28388200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr22:28386200-28389000	Weak transcription	Brain Angular Gyrus	brain
47	chr22:28386200-28405800	Strong transcription	Dnd41	blood
48	chr22:28386200-28416000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr22:28386400-28387800	Genic enhancers	Fetal Muscle Leg	muscle
50	chr22:28386400-28388200	Enhancers	Liver	Liver

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