Variant report

Variant	rs5753659
Chromosome Location	chr22:31893613-31893614
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	RUNX3	chr22:31891860-31894008	GM12878	blood:	n/a	n/a
2	STAT3	chr22:31893211-31893933	GM12878	blood:	n/a	n/a
3	KAP1	chr22:31892075-31893835	HEK293	kidney:	n/a	n/a
4	POLR2A	chr22:31893415-31893613	Hela-S3	cervix:	n/a	n/a
5	MXI1	chr22:31891626-31893666	GM12878	blood:	n/a	n/a
6	CREB1	chr22:31893409-31893973	GM12878	blood:	n/a	n/a
7	PML	chr22:31891297-31893892	GM12878	blood:	n/a	n/a
8	CUX1	chr22:31893438-31893656	GM12878	blood:	n/a	n/a
9	POLR2A	chr22:31891612-31893621	GM12878	blood:	n/a	n/a
10	ZNF263	chr22:31891889-31893693	HEK293-T-REx	kidney:	n/a	chr22:31892986-31892995 chr22:31892742-31892751
11	CREB1	chr22:31893219-31894054	GM12878	blood:	n/a	n/a
12	BATF	chr22:31893442-31893799	GM12878	blood:	n/a	n/a
13	SETDB1	chr22:31893357-31893906	U2OS	brain:	n/a	n/a
14	MTA3	chr22:31891303-31893982	GM12878	blood:	n/a	n/a
15	RUNX3	chr22:31893296-31893962	GM12878	blood:	n/a	n/a
16	TBP	chr22:31893268-31893900	GM12878	blood:	n/a	n/a
17	POLR2A	chr22:31891966-31893758	GM12878	blood:	n/a	n/a
18	TBL1XR1	chr22:31893513-31893766	GM12878	blood:	n/a	n/a
19	POLR2A	chr22:31893542-31893832	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr22:31892596..31895248-chr22:31897166..31900535,3	MCF-7	breast:
2	chr22:31892881..31894794-chr22:31897314..31900016,2	K562	blood:
3	chr22:31892695..31894776-chr22:32016253..32018919,2	K562	blood:

Variant related genes	Relation type
EIF4ENIF1	TF binding region

Extended variants
information (count: 80 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1018490	0.83[CHD][hapmap];0.81[JPT][hapmap]
rs13057504	0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1543416	0.82[JPT][hapmap]
rs16989527	0.88[YRI][hapmap]
rs16989611	1.00[YRI][hapmap]
rs16989642	1.00[YRI][hapmap]
rs16989647	1.00[YRI][hapmap]
rs16989655	1.00[YRI][hapmap]
rs16989698	0.85[LWK][hapmap];0.88[YRI][hapmap]
rs1968023	0.83[CEU][hapmap];0.84[TSI][hapmap]
rs2273249	0.91[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs2273251	0.91[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2899164	0.91[CHB][hapmap]
rs34538851	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34545960	0.80[AMR][1000 genomes]
rs4602315	0.85[LWK][hapmap]
rs4603880	0.87[TSI][hapmap]
rs4820983	0.82[JPT][hapmap]
rs5749267	0.83[AMR][1000 genomes]
rs5749268	0.83[AMR][1000 genomes]
rs5749270	0.83[AMR][1000 genomes]
rs5749283	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5749286	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5749291	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5749295	0.81[ASN][1000 genomes]
rs5749298	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5753601	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs5753609	0.81[TSI][hapmap]
rs5753610	0.83[AMR][1000 genomes]
rs5753612	0.80[AMR][1000 genomes]
rs5753613	0.83[AMR][1000 genomes]
rs5753615	0.87[AMR][1000 genomes]
rs5753618	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs5753621	0.88[CHB][hapmap];0.84[JPT][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs5753628	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5753631	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5753632	0.82[TSI][hapmap]
rs5753639	0.82[TSI][hapmap]
rs5753648	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5753661	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5753664	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5753665	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5753666	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5753669	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5753671	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5753686	0.82[JPT][hapmap]
rs5753698	1.00[CEU][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.97[TSI][hapmap]
rs5753723	0.83[CEU][hapmap]
rs5994394	0.83[AMR][1000 genomes]
rs5998058	1.00[CEU][hapmap];0.81[JPT][hapmap];0.93[TSI][hapmap]
rs5998067	1.00[CEU][hapmap];0.93[TSI][hapmap]
rs714909	0.87[TSI][hapmap]
rs7284622	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7285619	0.91[CHB][hapmap];0.86[JPT][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7293171	0.80[AMR][1000 genomes]
rs737887	0.84[TSI][hapmap]
rs8138525	1.00[CEU][hapmap];0.81[JPT][hapmap];0.93[TSI][hapmap]
rs8139625	0.87[AMR][1000 genomes]
rs8142121	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9606839	0.91[CHB][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes]
rs9606843	0.84[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.87[TSI][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9606846	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9606847	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9606848	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9606852	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9609286	0.87[AMR][1000 genomes]
rs9609295	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9609296	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9609297	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9609299	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9609301	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9609303	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9609304	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9609329	1.00[CEU][hapmap];0.95[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv459872	chr22:31833759-31977594	Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
3	nsv588894	chr22:31833759-31977594	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
4	nsv1060776	chr22:31869892-31900359	Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
5	esv3334530	chr22:31889221-31909085	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv1059314	chr22:31893613-31936088	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs5753659	SFI1	cis	Thyroid	GTEx

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31891600-31893800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr22:31891800-31893800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr22:31891800-31893800	Active TSS	Fetal Lung	lung
4	chr22:31892000-31893800	Active TSS	Fetal Heart	heart
5	chr22:31892200-31893800	Active TSS	Primary T cells fromperipheralblood	blood
6	chr22:31892600-31893800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
7	chr22:31892800-31894200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
8	chr22:31893000-31893800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr22:31893000-31893800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr22:31893000-31893800	Flanking Active TSS	HMEC	breast
11	chr22:31893000-31905200	Weak transcription	Aorta	Aorta
12	chr22:31893200-31893800	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr22:31893200-31893800	Enhancers	Spleen	Spleen
14	chr22:31893200-31894000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
15	chr22:31893200-31894000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
16	chr22:31893200-31894000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
17	chr22:31893200-31894200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr22:31893200-31903600	Weak transcription	Left Ventricle	heart
19	chr22:31893200-31912200	Weak transcription	Small Intestine	intestine
20	chr22:31893200-31934800	Weak transcription	Ovary	ovary
21	chr22:31893400-31893800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
22	chr22:31893400-31893800	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr22:31893400-31893800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
24	chr22:31893400-31893800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
25	chr22:31893400-31893800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr22:31893400-31893800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
27	chr22:31893400-31893800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr22:31893400-31893800	Enhancers	Brain Cingulate Gyrus	brain
29	chr22:31893400-31893800	Enhancers	Colon Smooth Muscle	Colon
30	chr22:31893400-31893800	ZNF genes & repeats	Fetal Muscle Leg	muscle
31	chr22:31893400-31893800	Flanking Active TSS	Fetal Thymus	thymus
32	chr22:31893400-31893800	Enhancers	Rectal Mucosa Donor 31	rectum
33	chr22:31893400-31893800	Enhancers	Sigmoid Colon	Sigmoid Colon
34	chr22:31893400-31893800	Flanking Active TSS	Thymus	Thymus
35	chr22:31893400-31893800	Flanking Active TSS	Hela-S3	cervix
36	chr22:31893400-31894000	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr22:31893400-31894000	Flanking Active TSS	Primary T cells from cord blood	blood
38	chr22:31893400-31894000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
39	chr22:31893400-31894000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
40	chr22:31893400-31894000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
41	chr22:31893400-31894000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
42	chr22:31893400-31894000	Enhancers	Brain Substantia Nigra	brain
43	chr22:31893400-31894000	Transcr. at gene 5' and 3'	Dnd41	blood
44	chr22:31893400-31894000	Active TSS	NH-A	brain
45	chr22:31893400-31894200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr22:31893400-31896600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr22:31893400-31897400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr22:31893400-31900000	Weak transcription	HSMM	muscle
49	chr22:31893400-31905200	Weak transcription	Fetal Intestine Large	intestine
50	chr22:31893400-31907200	Weak transcription	Fetal Intestine Small	intestine

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