Variant report

Variant	rs9625366
Chromosome Location	chr22:28329298-28329299
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	SRF	chr22:28328929-28329697	MCF-7	breast:	n/a	n/a
2	GATA3	chr22:28329114-28329640	MCF-7	breast:	n/a	n/a
3	POLR2A	chr22:28329115-28329302	ProgFib	skin:	n/a	n/a
4	NR2F2	chr22:28329162-28329686	MCF-7	breast:	n/a	n/a
5	STAT2	chr22:28329154-28329570	K562	blood:	n/a	chr22:28329304-28329319 chr22:28329354-28329369
6	SRF	chr22:28329052-28329660	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:28313401..28315263-chr22:28329069..28331136,2	K562	blood:
2	chr22:28327466..28330447-chr22:28330526..28332716,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HSCB-4	chr22:28328114-28329719	NONHSAT084630

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

Extended variants
information (count: 114 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs10154425	0.86[EUR][1000 genomes]
rs10483140	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10483142	0.81[EUR][1000 genomes]
rs10483143	0.81[EUR][1000 genomes]
rs118840	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12165651	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12165797	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12166023	0.85[EUR][1000 genomes]
rs12166077	0.91[EUR][1000 genomes]
rs12166158	0.86[EUR][1000 genomes]
rs12166256	0.86[EUR][1000 genomes]
rs12166389	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12166740	0.90[EUR][1000 genomes]
rs12166912	0.86[EUR][1000 genomes]
rs12166938	0.81[EUR][1000 genomes]
rs12167320	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12167829	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12168054	0.88[EUR][1000 genomes]
rs12168180	0.85[EUR][1000 genomes]
rs12168251	0.81[EUR][1000 genomes]
rs12168582	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12169097	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12169888	0.91[EUR][1000 genomes]
rs12169936	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12170022	0.86[EUR][1000 genomes]
rs12170953	0.91[EUR][1000 genomes]
rs12171104	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs138636	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs138637	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs138639	0.96[EUR][1000 genomes]
rs138640	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs138642	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs138651	0.91[EUR][1000 genomes]
rs138653	0.86[EUR][1000 genomes]
rs138654	0.91[EUR][1000 genomes]
rs138655	0.91[EUR][1000 genomes]
rs138656	0.91[EUR][1000 genomes]
rs138658	0.91[EUR][1000 genomes]
rs138660	0.91[EUR][1000 genomes]
rs138664	0.91[EUR][1000 genomes]
rs138665	0.91[EUR][1000 genomes]
rs138667	0.91[EUR][1000 genomes]
rs138669	0.84[EUR][1000 genomes]
rs138670	0.86[EUR][1000 genomes]
rs138671	0.91[EUR][1000 genomes]
rs138672	0.91[EUR][1000 genomes]
rs16985763	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16986037	0.86[EUR][1000 genomes]
rs16987005	0.86[EUR][1000 genomes]
rs17390800	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17407024	0.83[EUR][1000 genomes]
rs17483887	0.91[EUR][1000 genomes]
rs17484337	0.91[EUR][1000 genomes]
rs2745562	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28375646	0.91[EUR][1000 genomes]
rs470098	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs470102	0.91[EUR][1000 genomes]
rs470103	0.91[EUR][1000 genomes]
rs470104	0.91[EUR][1000 genomes]
rs55856549	0.81[EUR][1000 genomes]
rs56233401	0.86[EUR][1000 genomes]
rs57686964	0.86[EUR][1000 genomes]
rs58050941	0.86[EUR][1000 genomes]
rs58823697	0.86[EUR][1000 genomes]
rs7286519	0.91[EUR][1000 genomes]
rs7288331	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7289984	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][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	0.91[EUR][1000 genomes]
rs73880375	0.91[EUR][1000 genomes]
rs73880376	0.91[EUR][1000 genomes]
rs73880381	0.91[EUR][1000 genomes]
rs73880382	0.84[EUR][1000 genomes]
rs73880383	0.81[EUR][1000 genomes]
rs73880384	0.81[EUR][1000 genomes]
rs73880387	0.88[EUR][1000 genomes]
rs73880393	0.85[EUR][1000 genomes]
rs761323	0.86[EUR][1000 genomes]
rs8141163	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8141173	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9620752	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9620753	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9620755	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9620757	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9620762	0.91[EUR][1000 genomes]
rs9620764	0.91[EUR][1000 genomes]
rs9620768	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9620769	0.85[EUR][1000 genomes]
rs9620771	0.85[EUR][1000 genomes]
rs9625361	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625363	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625367	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625370	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625374	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625375	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625377	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9625387	0.91[EUR][1000 genomes]
rs9625388	0.91[EUR][1000 genomes]
rs9625390	0.91[EUR][1000 genomes]
rs9625391	0.90[EUR][1000 genomes]
rs9625393	0.81[EUR][1000 genomes]
rs9625395	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9625408	0.86[EUR][1000 genomes]
rs9625409	0.85[EUR][1000 genomes]
rs9625410	0.83[EUR][1000 genomes]
rs9625413	0.86[EUR][1000 genomes]
rs9625415	0.84[EUR][1000 genomes]
rs9625416	0.86[EUR][1000 genomes]
rs9625417	0.86[EUR][1000 genomes]
rs9625418	0.85[EUR][1000 genomes]
rs9625421	0.81[EUR][1000 genomes]
rs9985213	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28316200-28337400	Weak transcription	Ovary	ovary
2	chr22:28316400-28335000	Weak transcription	Colonic Mucosa	Colon
3	chr22:28316400-28336800	Weak transcription	Fetal Muscle Leg	muscle
4	chr22:28316400-28342600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr22:28316400-28358600	Weak transcription	Placenta	Placenta
6	chr22:28316400-28370200	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr22:28316400-28376800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr22:28316400-28378000	Weak transcription	Esophagus	oesophagus
9	chr22:28316600-28348400	Weak transcription	Brain Substantia Nigra	brain
10	chr22:28316800-28333800	Weak transcription	Brain Hippocampus Middle	brain
11	chr22:28316800-28336600	Weak transcription	Fetal Intestine Large	intestine
12	chr22:28316800-28340400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr22:28317000-28338800	Weak transcription	Fetal Intestine Small	intestine
14	chr22:28317000-28340800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr22:28317000-28348200	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr22:28317200-28336600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr22:28317600-28340800	Weak transcription	Thymus	Thymus
18	chr22:28317800-28342600	Weak transcription	Small Intestine	intestine
19	chr22:28317800-28345200	Weak transcription	HepG2	liver
20	chr22:28318600-28332400	Weak transcription	K562	blood
21	chr22:28318800-28382000	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr22:28319400-28334000	Weak transcription	Fetal Stomach	stomach
23	chr22:28319600-28340800	Weak transcription	Fetal Thymus	thymus
24	chr22:28319600-28358000	Weak transcription	Brain Germinal Matrix	brain
25	chr22:28319600-28383000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr22:28320800-28347800	Weak transcription	HUVEC	blood vessel
27	chr22:28321000-28354800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr22:28321200-28358400	Weak transcription	Fetal Muscle Trunk	muscle
29	chr22:28321400-28340400	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr22:28321400-28379000	Weak transcription	Primary B cells from cord blood	blood
31	chr22:28321600-28332200	Weak transcription	Fetal Brain Female	brain
32	chr22:28321600-28345000	Weak transcription	Fetal Lung	lung
33	chr22:28321800-28342800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr22:28322000-28365200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr22:28322000-28366200	Weak transcription	Primary hematopoietic stem cells	blood
36	chr22:28322200-28339600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr22:28322600-28329400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr22:28323000-28331000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr22:28323800-28346000	Weak transcription	Dnd41	blood
40	chr22:28326600-28330000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr22:28326800-28334600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr22:28326800-28368600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr22:28327000-28334000	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr22:28327000-28339200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr22:28327000-28348000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr22:28327000-28348400	Weak transcription	Rectal Smooth Muscle	rectum
47	chr22:28327200-28330200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr22:28327200-28333600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr22:28327200-28339200	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr22:28327400-28329400	Active TSS	Adipose Nuclei	Adipose

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