Variant report

Variant	rs2283879
Chromosome Location	chr22:31638448-31638449
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:31636927..31638893-chr22:31647467..31649830,2	K562	blood:
2	chr22:31636192..31639779-chr22:31685057..31687431,3	MCF-7	breast:
3	chr22:31362595..31365185-chr22:31636679..31638465,2	MCF-7	breast:
4	chr22:31606906..31609488-chr22:31638406..31640879,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000133422	Chromatin interaction
ENSG00000182541	Chromatin interaction
ENSG00000100100	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1034588	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1034589	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12152166	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13054220	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13056485	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs131205	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13158	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1858821	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2040533	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2073857	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2078803	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2079431	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2106294	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2228619	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2232170	0.85[CEU][hapmap]
rs2232176	0.85[CEU][hapmap]
rs2273249	0.95[CEU][hapmap]
rs2283881	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2413031	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2413032	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2413033	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2413034	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2413035	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2413046	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2413047	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2413049	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2899164	0.95[CEU][hapmap]
rs4141404	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4299418	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4603880	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4820042	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4820043	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4820951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4820955	1.00[CEU][hapmap]
rs4820962	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4820963	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5749224	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs5749229	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5749243	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5753500	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5753505	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs5753507	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs5753521	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5753543	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5753601	0.95[CEU][hapmap]
rs5753609	0.90[CEU][hapmap]
rs59315359	0.81[EUR][1000 genomes]
rs5997902	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5997912	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5997913	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs5997933	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5997939	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5997949	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs71324184	0.83[EUR][1000 genomes]
rs714909	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs715510	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7287267	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs737684	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs737887	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs737888	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8135344	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8135347	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8138596	0.83[EUR][1000 genomes]
rs8139160	0.81[EUR][1000 genomes]
rs9606830	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9606831	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9606839	0.95[CEU][hapmap]
rs9609254	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9609257	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9609264	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9609265	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9609266	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9609267	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9609268	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9621235	0.88[EUR][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
rs2283879	SFI1	cis	Thyroid	GTEx
rs2283879	DRG1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31608800-31639800	Weak transcription	Aorta	Aorta
2	chr22:31609600-31639200	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr22:31625600-31639800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr22:31625800-31639600	Weak transcription	Esophagus	oesophagus
5	chr22:31626600-31639800	Weak transcription	NHDF-Ad	bronchial
6	chr22:31626600-31643800	Weak transcription	Left Ventricle	heart
7	chr22:31626600-31643800	Weak transcription	Spleen	Spleen
8	chr22:31626800-31639600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr22:31627600-31639000	Weak transcription	Fetal Muscle Leg	muscle
10	chr22:31627600-31639600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr22:31627600-31639800	Weak transcription	Stomach Smooth Muscle	stomach
12	chr22:31627600-31640000	Weak transcription	Fetal Heart	heart
13	chr22:31627600-31640800	Weak transcription	Liver	Liver
14	chr22:31627800-31639400	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr22:31627800-31639600	Weak transcription	Colon Smooth Muscle	Colon
16	chr22:31627800-31640000	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr22:31627800-31640800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr22:31627800-31640800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr22:31627800-31643200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr22:31627800-31643400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr22:31627800-31643400	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr22:31628000-31643800	Weak transcription	Brain Hippocampus Middle	brain
23	chr22:31629800-31639200	Weak transcription	Psoas Muscle	Psoas
24	chr22:31629800-31639400	Weak transcription	Fetal Thymus	thymus
25	chr22:31629800-31639600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr22:31631000-31639600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr22:31631600-31643800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr22:31632000-31643200	Weak transcription	Colonic Mucosa	Colon
29	chr22:31632400-31640600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr22:31634400-31639800	Enhancers	Fetal Intestine Large	intestine
31	chr22:31634400-31640400	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr22:31634400-31643800	Weak transcription	Primary B cells from peripheral blood	blood
33	chr22:31634600-31640200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr22:31634800-31641200	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr22:31634800-31643600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr22:31635000-31641200	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr22:31635600-31639400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr22:31635600-31639600	Enhancers	Osteobl	bone
39	chr22:31635600-31639800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr22:31635800-31639200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr22:31635800-31639200	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr22:31635800-31639400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr22:31635800-31639600	Enhancers	Muscle Satellite Cultured Cells	--
44	chr22:31635800-31640400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr22:31636000-31639600	Weak transcription	Placenta	Placenta
46	chr22:31636200-31639400	Enhancers	A549	lung
47	chr22:31636200-31643800	Weak transcription	Fetal Lung	lung
48	chr22:31636200-31644200	Weak transcription	Ovary	ovary
49	chr22:31636400-31642200	Strong transcription	Primary neutrophils fromperipheralblood	blood
50	chr22:31636600-31640200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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