Variant report

Variant	rs5753609
Chromosome Location	chr22:31819212-31819213
allele	A/G
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	MAFF	chr22:31819204-31819222	K562	blood:	n/a	n/a
2	POLR2A	chr22:31819184-31819504	GM12891	blood:	n/a	n/a
3	MAFF	chr22:31819095-31819295	HepG2	liver:	n/a	chr22:31819228-31819246
4	MAFK	chr22:31819089-31819393	HepG2	liver:	n/a	chr22:31819230-31819241 chr22:31819230-31819245 chr22:31819231-31819251 chr22:31819230-31819246

No.	Distal block	Cell Line	Cell type
1	22:31807204-31822350..22:31836635-31847259	K562	blood:
2	22:31807204-31822350..22:32292186-32294405	K562	blood:
3	22:31807204-31822350..22:32012966-32043914	K562	blood:
4	22:31807204-31822350..22:31978142-31983723	GM12878	blood:

Variant related genes	Relation type
DRG1	TF binding region
ENSG00000100150	Chromatin interaction
ENSG00000198089	Chromatin interaction
ENSG00000184708	Chromatin interaction
ENSG00000241878	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs1001599	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13057504	0.82[EUR][1000 genomes]
rs1858821	0.90[CEU][hapmap];0.81[GIH][hapmap];0.85[TSI][hapmap]
rs2040533	0.90[CEU][hapmap]
rs2073857	0.90[CEU][hapmap];0.81[GIH][hapmap];0.85[TSI][hapmap]
rs2078803	0.90[CEU][hapmap]
rs2103853	0.83[MKK][hapmap]
rs2106294	0.90[CEU][hapmap];0.81[GIH][hapmap];0.85[TSI][hapmap]
rs2228619	0.90[CEU][hapmap]
rs2273249	0.95[CEU][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes]
rs2273251	0.95[CEU][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes]
rs2283879	0.90[CEU][hapmap]
rs2899164	0.95[CEU][hapmap];0.82[JPT][hapmap];0.91[EUR][1000 genomes]
rs34545960	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4141404	0.90[CEU][hapmap];0.81[GIH][hapmap];0.85[TSI][hapmap]
rs4603880	0.90[CEU][hapmap];0.88[TSI][hapmap]
rs4820043	0.90[CEU][hapmap];0.81[GIH][hapmap];0.85[TSI][hapmap]
rs4820955	0.90[CEU][hapmap]
rs4820963	0.90[CEU][hapmap]
rs5749265	0.92[EUR][1000 genomes]
rs5749267	0.93[EUR][1000 genomes]
rs5749268	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5749270	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5749272	0.83[MEX][hapmap]
rs5749279	0.83[AMR][1000 genomes]
rs5749286	0.82[TSI][hapmap]
rs5753521	0.90[CEU][hapmap]
rs5753543	0.90[CEU][hapmap]
rs5753597	0.92[EUR][1000 genomes]
rs5753601	0.95[CEU][hapmap];0.86[JPT][hapmap];0.92[EUR][1000 genomes]
rs5753610	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5753612	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5753613	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5753615	0.83[EUR][1000 genomes]
rs5753618	0.82[JPT][hapmap]
rs5753621	0.81[JPT][hapmap]
rs5753628	0.80[EUR][1000 genomes]
rs5753632	0.83[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs5753639	0.83[ASW][hapmap];0.95[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs5753659	0.81[TSI][hapmap]
rs5753669	0.82[TSI][hapmap]
rs5753671	0.82[TSI][hapmap]
rs5994394	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5997977	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs695438	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71324184	0.83[EUR][1000 genomes]
rs714909	0.90[CEU][hapmap];0.81[GIH][hapmap];0.88[TSI][hapmap]
rs715510	0.90[CEU][hapmap]
rs7285619	0.95[CEU][hapmap];0.81[GIH][hapmap];0.82[JPT][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs7293171	0.92[EUR][1000 genomes]
rs737684	0.90[CEU][hapmap]
rs737887	0.90[CEU][hapmap];0.81[GIH][hapmap];0.85[TSI][hapmap]
rs738657	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8138596	0.83[EUR][1000 genomes]
rs8141150	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9606830	0.90[CEU][hapmap]
rs9606839	0.95[CEU][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9606843	0.95[CEU][hapmap];0.81[GIH][hapmap];0.82[JPT][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs9606848	0.82[TSI][hapmap]
rs9609264	0.90[CEU][hapmap]
rs9609268	0.82[EUR][1000 genomes]
rs9609276	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9609277	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9609296	0.85[TSI][hapmap]
rs9609304	0.82[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834176	chr22:31682426-31864701	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
2	nsv1063634	chr22:31797004-31921254	Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs5753609	SFI1	cis	Thyroid	GTEx
rs5753609	PISD	cis	cerebellum	SCAN
rs5753609	MN1	cis	parietal	SCAN
rs5753609	SFI1	cis	cerebellum	SCAN
rs5753609	DRG1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31796600-31821200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr22:31796600-31830000	Weak transcription	Stomach Mucosa	stomach
3	chr22:31796800-31822400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr22:31796800-31835600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr22:31797000-31832000	Strong transcription	Fetal Muscle Leg	muscle
6	chr22:31797000-31836600	Strong transcription	Placenta	Placenta
7	chr22:31797000-31884400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr22:31797000-31884400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr22:31797200-31826800	Strong transcription	Liver	Liver
10	chr22:31797200-31832600	Strong transcription	Fetal Intestine Small	intestine
11	chr22:31797200-31845400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr22:31797200-31846200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr22:31797200-31846400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr22:31797200-31860600	Strong transcription	Fetal Stomach	stomach
15	chr22:31797400-31821200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr22:31797400-31846800	Strong transcription	Duodenum Mucosa	Duodenum
17	chr22:31797600-31828000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr22:31797600-31835800	Strong transcription	Fetal Muscle Trunk	muscle
19	chr22:31797800-31821600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr22:31797800-31832200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr22:31797800-31844800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr22:31797800-31846800	Strong transcription	Primary T cells fromperipheralblood	blood
23	chr22:31798000-31831800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr22:31798200-31827000	Strong transcription	Stomach Smooth Muscle	stomach
25	chr22:31798200-31831200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr22:31798600-31821000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr22:31799000-31845400	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr22:31799200-31846600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr22:31800200-31821000	Weak transcription	Fetal Brain Male	brain
30	chr22:31803400-31822000	Weak transcription	Fetal Heart	heart
31	chr22:31803600-31844600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr22:31804600-31847000	Strong transcription	Sigmoid Colon	Sigmoid Colon
33	chr22:31805000-31844800	Strong transcription	Primary B cells from peripheral blood	blood
34	chr22:31805600-31844800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr22:31806800-31842400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
36	chr22:31807800-31821400	Weak transcription	Right Ventricle	heart
37	chr22:31807800-31822200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr22:31812000-31842000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr22:31812200-31821200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr22:31812400-31821000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr22:31812400-31821000	Weak transcription	Rectal Smooth Muscle	rectum
42	chr22:31812600-31821400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr22:31813600-31845000	Strong transcription	Fetal Thymus	thymus
44	chr22:31813800-31824200	Strong transcription	Spleen	Spleen
45	chr22:31814000-31819600	Strong transcription	Primary T cells from cord blood	blood
46	chr22:31814000-31838000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr22:31814000-31841200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr22:31814000-31846400	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr22:31814200-31846800	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr22:31814400-31832000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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