Variant report

Variant	rs11089512
Chromosome Location	chr22:31884033-31884034
allele	C/T
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	SPI1	chr22:31883898-31884232	HL-60	blood:	n/a	chr22:31884030-31884037

No.	Distal block	Cell Line	Cell type
1	chr14:60714772..60717731-chr22:31883101..31885338,2	MCF-7	breast:
2	22:31864703-31891033..22:31936958-31958600	GM12878	blood:
3	chr22:31883675..31887496-chr22:32025240..32029301,5	K562	blood:
4	22:31864703-31891033..22:31930706-31935473	GM12878	blood:
5	22:31864703-31891033..22:32347255-32351014	K562	blood:
6	chr22:31742290..31744009-chr22:31883766..31886602,4	MCF-7	breast:

Variant related genes	Relation type
SFI1	TF binding region
ENSG00000213888	Chromatin interaction
ENSG00000254718	Chromatin interaction
ENSG00000241878	Chromatin interaction
ENSG00000214093	Chromatin interaction
ENSG00000229169	Chromatin interaction
ENSG00000100614	Chromatin interaction
ENSG00000238910	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1044085	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap]
rs11089514	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11089515	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12166823	0.83[TSI][hapmap]
rs12170867	1.00[CEU][hapmap];0.86[JPT][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12485048	0.92[TSI][hapmap]
rs12628465	1.00[MKK][hapmap]
rs13056823	0.87[ASN][1000 genomes]
rs17821102	0.90[CHB][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2024747	1.00[ASW][hapmap];0.90[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2092905	0.86[JPT][hapmap]
rs2295242	0.86[JPT][hapmap]
rs2387	0.86[JPT][hapmap]
rs2413053	0.94[ASN][1000 genomes]
rs3818134	0.91[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs4535154	0.90[ASN][1000 genomes]
rs4820051	0.90[CEU][hapmap]
rs4820976	0.87[ASN][1000 genomes]
rs4820978	0.85[ASN][1000 genomes]
rs4820979	0.95[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs4820980	0.95[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs4820981	0.82[ASN][1000 genomes]
rs5749278	0.83[CHB][hapmap];0.81[AFR][1000 genomes]
rs5749280	0.90[CHB][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs5749287	0.86[ASN][1000 genomes]
rs5749293	1.00[ASW][hapmap];0.90[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5749297	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5749301	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs5749303	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs5749306	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs5753559	1.00[MKK][hapmap]
rs5753620	1.00[ASW][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[TSI][hapmap]
rs5753622	1.00[ASW][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs5753627	0.90[CHB][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs5753633	1.00[ASW][hapmap];0.89[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs5753635	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs5753647	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5753650	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5753657	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5753667	1.00[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs5753675	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5753677	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5753680	0.84[ASN][1000 genomes]
rs5753681	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5753684	0.84[ASN][1000 genomes]
rs5753687	0.83[ASN][1000 genomes]
rs59285943	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5998011	0.90[ASN][1000 genomes]
rs5998032	0.84[ASN][1000 genomes]
rs5998087	1.00[MKK][hapmap]
rs7288464	0.89[ASN][1000 genomes]
rs738656	0.91[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs738702	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9306266	0.93[ASN][1000 genomes]
rs9306268	1.00[MKK][hapmap]
rs9621269	0.86[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9621291	0.82[EUR][1000 genomes]
rs9621305	0.83[TSI][hapmap]

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	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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31797000-31884400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr22:31797000-31884400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr22:31823600-31884600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr22:31854800-31884600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr22:31856800-31885000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr22:31858400-31884600	Weak transcription	Psoas Muscle	Psoas
7	chr22:31859400-31884800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr22:31860200-31884800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr22:31864400-31884400	Weak transcription	Brain Substantia Nigra	brain
10	chr22:31864400-31884600	Weak transcription	Aorta	Aorta
11	chr22:31864600-31884600	Weak transcription	Right Ventricle	heart
12	chr22:31867600-31884600	Weak transcription	Pancreas	Pancrea
13	chr22:31868800-31884200	Strong transcription	HSMM	muscle
14	chr22:31870800-31884400	Strong transcription	Fetal Thymus	thymus
15	chr22:31871000-31884400	Strong transcription	Placenta	Placenta
16	chr22:31872200-31884200	Weak transcription	Hela-S3	cervix
17	chr22:31872600-31884200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr22:31872600-31884400	Strong transcription	Fetal Muscle Trunk	muscle
19	chr22:31872800-31884400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr22:31872800-31884400	Strong transcription	Fetal Muscle Leg	muscle
21	chr22:31873400-31884200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr22:31873600-31884200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr22:31873600-31884200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr22:31873600-31884200	Strong transcription	Osteobl	bone
25	chr22:31874400-31884600	Weak transcription	Stomach Mucosa	stomach
26	chr22:31875200-31884200	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr22:31875200-31884400	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr22:31875200-31884400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr22:31875800-31884600	Weak transcription	Colonic Mucosa	Colon
30	chr22:31876000-31884400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr22:31877000-31884400	Strong transcription	HUES48 Cell Line	embryonic stem cell
32	chr22:31877000-31884400	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr22:31878000-31884600	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr22:31878000-31885000	Weak transcription	Esophagus	oesophagus
35	chr22:31878200-31884200	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr22:31878400-31884400	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr22:31878400-31884600	Weak transcription	Small Intestine	intestine
38	chr22:31878400-31884600	Weak transcription	Spleen	Spleen
39	chr22:31878600-31884200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr22:31879200-31884200	Strong transcription	Brain Inferior Temporal Lobe	brain
41	chr22:31879800-31884600	Weak transcription	Thymus	Thymus
42	chr22:31880000-31884600	Weak transcription	Fetal Brain Male	brain
43	chr22:31880400-31884600	Weak transcription	HSMMtube	muscle
44	chr22:31881200-31884200	Weak transcription	Brain Angular Gyrus	brain
45	chr22:31881400-31884200	Weak transcription	Brain Anterior Caudate	brain
46	chr22:31881400-31884200	Weak transcription	K562	blood
47	chr22:31881400-31884400	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr22:31881400-31884400	Weak transcription	Rectal Smooth Muscle	rectum
49	chr22:31881600-31884200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr22:31881600-31884200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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