Variant report

Variant	rs5997909
Chromosome Location	chr22:31591228-31591229
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:31589872..31591421-chr22:31606722..31609193,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000182541	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs11703927	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12166373	0.91[EUR][1000 genomes]
rs12167361	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13056815	0.87[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs13057841	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs131200	0.88[EUR][1000 genomes]
rs131202	0.86[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs131209	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs131213	0.84[EUR][1000 genomes]
rs131219	0.83[EUR][1000 genomes]
rs140074	0.89[EUR][1000 genomes]
rs140077	0.87[EUR][1000 genomes]
rs2009132	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2013254	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2027982	0.84[AMR][1000 genomes]
rs2413048	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28715	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28716	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28813120	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34873968	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4820045	0.80[EUR][1000 genomes]
rs4820961	0.83[AFR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4820969	0.83[EUR][1000 genomes]
rs5753558	0.86[EUR][1000 genomes]
rs5753576	0.83[EUR][1000 genomes]
rs5994376	0.91[ASN][1000 genomes]
rs5997887	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5997900	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5997919	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5997929	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5997932	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5997938	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5997960	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs713947	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7285171	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7286648	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7287402	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7288643	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7288735	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7289189	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7289337	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs739427	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8141987	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8143002	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9606835	0.80[EUR][1000 genomes]
rs9619169	0.85[EUR][1000 genomes]
rs9619187	0.90[EUR][1000 genomes]
rs9621216	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9621221	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9621227	0.90[AFR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv459871	chr22:31551160-31680624	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
2	nsv588893	chr22:31551160-31680624	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
3	nsv1067003	chr22:31558663-31697093	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs5997909	DRG1	Cis_1M	lymphoblastoid	RTeQTL
rs5997909	SFI1	cis	Thyroid	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31557400-31595200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr22:31557400-31597800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr22:31557600-31591800	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr22:31558600-31591400	Weak transcription	Primary hematopoietic stem cells	blood
5	chr22:31558800-31606000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr22:31569800-31591600	Weak transcription	Small Intestine	intestine
7	chr22:31570000-31606400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr22:31570400-31597800	Weak transcription	HUVEC	blood vessel
9	chr22:31572200-31600000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr22:31574400-31601600	Weak transcription	Fetal Heart	heart
11	chr22:31575800-31591600	Weak transcription	NH-A	brain
12	chr22:31575800-31602600	Weak transcription	Stomach Mucosa	stomach
13	chr22:31575800-31607600	Weak transcription	Hela-S3	cervix
14	chr22:31576000-31591400	Weak transcription	Fetal Kidney	kidney
15	chr22:31576000-31607800	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr22:31576000-31607800	Weak transcription	A549	lung
17	chr22:31578800-31591400	Weak transcription	HSMM	muscle
18	chr22:31579200-31607400	Weak transcription	K562	blood
19	chr22:31580800-31607600	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr22:31581000-31592800	Strong transcription	Fetal Muscle Leg	muscle
21	chr22:31581000-31593000	Strong transcription	Primary T cells from cord blood	blood
22	chr22:31581000-31599200	Strong transcription	Primary T helper cells PMA-I stimulated	--
23	chr22:31581400-31607800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr22:31582400-31602400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr22:31582600-31594000	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr22:31582800-31594200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr22:31582800-31603600	Strong transcription	Liver	Liver
28	chr22:31583000-31598800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr22:31583600-31591400	Weak transcription	Aorta	Aorta
30	chr22:31583600-31591400	Weak transcription	Gastric	stomach
31	chr22:31583600-31591400	Weak transcription	Pancreas	Pancrea
32	chr22:31584000-31608200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr22:31584200-31591400	Weak transcription	Colonic Mucosa	Colon
34	chr22:31584200-31591400	Weak transcription	Rectal Smooth Muscle	rectum
35	chr22:31584800-31595200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr22:31584800-31597800	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr22:31585600-31592200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr22:31585600-31593000	Strong transcription	Fetal Intestine Large	intestine
39	chr22:31585600-31599200	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr22:31585600-31599800	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr22:31585600-31601200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr22:31586000-31593000	Strong transcription	Primary B cells from cord blood	blood
43	chr22:31586000-31603800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr22:31586200-31591400	Weak transcription	Ovary	ovary
45	chr22:31586400-31595200	Weak transcription	HMEC	breast
46	chr22:31586600-31592800	Strong transcription	Thymus	Thymus
47	chr22:31587000-31599200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr22:31587000-31602200	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr22:31587400-31591400	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr22:31587600-31596000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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