Variant report

Variant	rs5997902
Chromosome Location	chr22:31583007-31583008
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	chr22:31582003..31584515-chr22:31685360..31688125,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100100	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1034588	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1034589	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13054220	0.82[EUR][1000 genomes]
rs13158	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1858821	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2040533	0.90[EUR][1000 genomes]
rs2073857	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2078803	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2079431	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2106294	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2228619	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2283879	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2283881	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2413031	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2413032	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2413033	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2413034	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2413035	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2413046	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2413047	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2413049	0.88[EUR][1000 genomes]
rs4141404	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4299418	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4603880	0.83[EUR][1000 genomes]
rs4820042	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4820043	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4820951	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4820962	0.83[EUR][1000 genomes]
rs4820963	0.85[EUR][1000 genomes]
rs5749224	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5749229	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5749243	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs5753500	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5753505	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs5753507	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5753521	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5753543	0.89[EUR][1000 genomes]
rs5997912	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5997913	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs5997933	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs5997939	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs714909	0.83[EUR][1000 genomes]
rs715510	0.85[EUR][1000 genomes]
rs7287267	0.83[EUR][1000 genomes]
rs737684	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs737887	0.86[EUR][1000 genomes]
rs737888	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8135344	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8135347	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9606830	0.82[EUR][1000 genomes]
rs9606831	0.83[EUR][1000 genomes]
rs9609254	0.81[EUR][1000 genomes]
rs9609264	0.82[EUR][1000 genomes]
rs9609265	0.83[EUR][1000 genomes]
rs9609266	0.83[EUR][1000 genomes]
rs9609267	0.83[EUR][1000 genomes]
rs9609268	0.80[EUR][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
rs5997902	DRG1	Cis_1M	lymphoblastoid	RTeQTL
rs5997902	SFI1	cis	Thyroid	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31557200-31591200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr22:31557400-31595200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr22:31557400-31597800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr22:31557600-31591800	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr22:31557800-31587000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr22:31557800-31588400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr22:31558600-31591400	Weak transcription	Primary hematopoietic stem cells	blood
8	chr22:31558800-31591200	Weak transcription	Fetal Brain Male	brain
9	chr22:31558800-31606000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr22:31562400-31583200	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr22:31569600-31583200	Weak transcription	Brain Anterior Caudate	brain
12	chr22:31569800-31591600	Weak transcription	Small Intestine	intestine
13	chr22:31570000-31606400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr22:31570400-31586800	Strong transcription	Fetal Stomach	stomach
15	chr22:31570400-31597800	Weak transcription	HUVEC	blood vessel
16	chr22:31572200-31600000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr22:31574000-31583200	Weak transcription	Duodenum Mucosa	Duodenum
18	chr22:31574200-31590800	Weak transcription	Brain Substantia Nigra	brain
19	chr22:31574400-31601600	Weak transcription	Fetal Heart	heart
20	chr22:31574600-31583200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr22:31574800-31587200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr22:31575800-31588600	Weak transcription	Colon Smooth Muscle	Colon
23	chr22:31575800-31588600	Weak transcription	NHLF	lung
24	chr22:31575800-31591600	Weak transcription	NH-A	brain
25	chr22:31575800-31602600	Weak transcription	Stomach Mucosa	stomach
26	chr22:31575800-31607600	Weak transcription	Hela-S3	cervix
27	chr22:31576000-31583200	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr22:31576000-31583400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr22:31576000-31583400	Weak transcription	HMEC	breast
30	chr22:31576000-31583600	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr22:31576000-31591200	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr22:31576000-31591400	Weak transcription	Fetal Kidney	kidney
33	chr22:31576000-31607800	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr22:31576000-31607800	Weak transcription	A549	lung
35	chr22:31576400-31584800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr22:31577800-31587000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr22:31577800-31588600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr22:31578800-31591400	Weak transcription	HSMM	muscle
39	chr22:31579000-31584800	Strong transcription	Lung	lung
40	chr22:31579200-31584400	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr22:31579200-31607400	Weak transcription	K562	blood
42	chr22:31579400-31588600	Weak transcription	Right Ventricle	heart
43	chr22:31580600-31587000	Strong transcription	Fetal Intestine Small	intestine
44	chr22:31580800-31587200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr22:31580800-31607600	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr22:31581000-31583600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr22:31581000-31584200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr22:31581000-31584200	Strong transcription	Fetal Lung	lung
49	chr22:31581000-31584800	Strong transcription	Fetal Intestine Large	intestine
50	chr22:31581000-31587400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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