Variant report

Variant	rs5997939
Chromosome Location	chr22:31677130-31677131
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:31675823..31681003-chr22:31682955..31686672,6	MCF-7	breast:
2	chr22:31653707..31656305-chr22:31675545..31677942,2	K562	blood:
3	chr22:31676896..31678671-chr22:31685121..31687949,2	K562	blood:
4	chr22:31675502..31680244-chr22:31686864..31689429,4	MCF-7	breast:
5	chr22:31674730..31677277-chr22:31677970..31680795,3	K562	blood:

Variant related genes	Relation type
ENSG00000182541	Chromatin interaction
ENSG00000100100	Chromatin interaction
ENSG00000228839	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1034588	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1034589	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs12152166	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13054220	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs131205	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1858821	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2040533	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2073857	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2078803	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2079431	0.89[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2106294	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2228619	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2283879	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2283881	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2413031	0.80[EUR][1000 genomes]
rs2413032	0.85[EUR][1000 genomes]
rs2413033	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2413034	0.89[EUR][1000 genomes]
rs2413035	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2413046	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2413047	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2413049	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4141404	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4299418	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4603880	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4820042	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4820043	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4820951	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4820962	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4820963	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5749224	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs5749229	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5749243	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5753500	0.88[EUR][1000 genomes]
rs5753505	0.82[EUR][1000 genomes]
rs5753507	0.87[EUR][1000 genomes]
rs5753521	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5753543	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59315359	0.81[EUR][1000 genomes]
rs5997902	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5997912	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5997913	0.89[EUR][1000 genomes]
rs5997933	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5997949	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs71324184	0.83[EUR][1000 genomes]
rs714909	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs715510	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7287267	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs737684	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs737887	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs737888	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8135344	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8135347	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8138596	0.82[EUR][1000 genomes]
rs8139160	0.81[EUR][1000 genomes]
rs9606830	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9606831	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9609254	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9609257	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9609264	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9609265	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9609266	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9609267	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9609268	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9621235	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	nsv1058844	chr22:31597104-31725296	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS 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
rs5997939	SFI1	cis	Thyroid	GTEx
rs5997939	DRG1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31645000-31677600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr22:31650200-31679200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr22:31652800-31679400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr22:31654000-31680400	Strong transcription	Lung	lung
5	chr22:31654000-31685600	Strong transcription	Fetal Stomach	stomach
6	chr22:31654200-31677200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr22:31654200-31680200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr22:31654200-31680400	Strong transcription	Sigmoid Colon	Sigmoid Colon
9	chr22:31654400-31679600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr22:31655400-31680800	Weak transcription	K562	blood
11	chr22:31657800-31681200	Strong transcription	Adipose Nuclei	Adipose
12	chr22:31659000-31685600	Weak transcription	Psoas Muscle	Psoas
13	chr22:31659400-31678600	Strong transcription	Fetal Muscle Leg	muscle
14	chr22:31661400-31677800	Weak transcription	A549	lung
15	chr22:31661800-31677600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr22:31665600-31679400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr22:31665800-31678800	Strong transcription	Fetal Muscle Trunk	muscle
18	chr22:31666000-31682600	Strong transcription	Skeletal Muscle Female	skeletal muscle
19	chr22:31666000-31684200	Strong transcription	Aorta	Aorta
20	chr22:31667000-31684600	Weak transcription	Right Atrium	heart
21	chr22:31667400-31677200	Strong transcription	Dnd41	blood
22	chr22:31668400-31681200	Strong transcription	NHLF	lung
23	chr22:31668800-31680400	Strong transcription	Duodenum Smooth Muscle	Duodenum
24	chr22:31669000-31678800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr22:31669000-31679400	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr22:31669000-31680200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr22:31669000-31680400	Strong transcription	Brain Anterior Caudate	brain
28	chr22:31669000-31682200	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr22:31669000-31682400	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr22:31669000-31685600	Weak transcription	Fetal Brain Male	brain
31	chr22:31669000-31686000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr22:31669200-31682600	Strong transcription	Stomach Smooth Muscle	stomach
33	chr22:31669400-31679000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr22:31669600-31680400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr22:31670000-31680600	Strong transcription	Primary B cells from peripheral blood	blood
36	chr22:31670600-31681000	Genic enhancers	Primary T cells fromperipheralblood	blood
37	chr22:31671200-31684600	Weak transcription	Fetal Heart	heart
38	chr22:31671400-31677800	Weak transcription	Ovary	ovary
39	chr22:31671400-31679200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr22:31671400-31680200	Strong transcription	Rectal Mucosa Donor 29	rectum
41	chr22:31671600-31679400	Strong transcription	Fetal Intestine Large	intestine
42	chr22:31671600-31679600	Strong transcription	Fetal Intestine Small	intestine
43	chr22:31671600-31681200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr22:31671800-31677600	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr22:31671800-31681000	Strong transcription	Rectal Mucosa Donor 31	rectum
46	chr22:31671800-31686200	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr22:31672000-31678000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr22:31672000-31680400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr22:31672600-31677400	Weak transcription	Small Intestine	intestine
50	chr22:31672600-31685600	Strong transcription	Brain Germinal Matrix	brain

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