Variant report

Variant	rs568423
Chromosome Location	chr11:65855678-65855679
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:65847605..65852889-chr11:65853586..65858030,6	MCF-7	breast:
2	chr11:65848858..65851939-chr11:65855053..65858345,4	K562	blood:
3	chr11:65845058..65846720-chr11:65854451..65856347,2	K562	blood:

Variant related genes	Relation type
ENSG00000175115	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10896065	1.00[MEX][hapmap]
rs1151532	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1190945	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1190946	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1191715	0.96[AFR][1000 genomes]
rs1203551	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1203552	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1203749	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1203750	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1203801	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1630638	0.96[AFR][1000 genomes]
rs1783562	0.92[AFR][1000 genomes]
rs1783732	1.00[YRI][hapmap]
rs2430981	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2452687	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3016315	0.85[AFR][1000 genomes]
rs3017606	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4523703	0.83[YRI][hapmap]
rs471203	1.00[MEX][hapmap]
rs471709	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs472853	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs475817	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs477001	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs485547	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4930169	1.00[MEX][hapmap]
rs4930332	0.96[AFR][1000 genomes]
rs502898	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs504456	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs505412	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs505642	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs510398	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs512316	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs515778	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs519911	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs527279	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs532265	0.86[AFR][1000 genomes]
rs541954	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs547282	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs547892	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs549228	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs551652	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs555527	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs555826	1.00[ASW][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs559298	0.84[ASW][hapmap];1.00[YRI][hapmap]
rs560105	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs560983	0.83[AFR][1000 genomes]
rs561199	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs561869	1.00[ASW][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs565921	1.00[MEX][hapmap]
rs567414	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs571368	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs572697	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs577301	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs581247	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6591196	0.92[AFR][1000 genomes]
rs693382	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7934588	0.89[AFR][1000 genomes]
rs7940700	1.00[MEX][hapmap]
rs7947668	0.96[AFR][1000 genomes]
rs948358	0.82[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap]
rs948477	1.00[YRI][hapmap];0.96[AFR][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	nsv948711	chr11:65692760-65949674	Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
2	esv3335923	chr11:65741698-66175759	Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
3	esv1819302	chr11:65787660-66007018	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
4	esv3407551	chr11:65794503-66158322	Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs568423	LOC404266	trans	lymphoblastoid	seeQTL

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65840600-65870600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr11:65842200-65867800	Weak transcription	Ovary	ovary
3	chr11:65845800-65868800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr11:65848400-65874200	Weak transcription	Fetal Muscle Leg	muscle
5	chr11:65849200-65879600	Weak transcription	Aorta	Aorta
6	chr11:65849400-65856200	Enhancers	Primary T cells fromperipheralblood	blood
7	chr11:65849400-65858000	Enhancers	Primary B cells from peripheral blood	blood
8	chr11:65849400-65858800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
9	chr11:65849600-65856800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr11:65849600-65857000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr11:65849600-65858600	Enhancers	Primary T helper naive cells from peripheral blood	blood
12	chr11:65849800-65857800	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr11:65849800-65858200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr11:65849800-65867600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr11:65850000-65855800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
16	chr11:65850200-65866200	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr11:65851200-65864600	Weak transcription	NHEK	skin
18	chr11:65851200-65867600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr11:65851400-65856000	Weak transcription	Fetal Brain Female	brain
20	chr11:65851600-65858600	Weak transcription	Fetal Intestine Small	intestine
21	chr11:65851600-65867800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr11:65851600-65868200	Weak transcription	Stomach Smooth Muscle	stomach
23	chr11:65851600-65882800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr11:65851800-65855800	Weak transcription	Fetal Brain Male	brain
25	chr11:65851800-65856600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr11:65851800-65858200	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr11:65851800-65867800	Weak transcription	Esophagus	oesophagus
28	chr11:65851800-65872000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr11:65851800-65878800	Weak transcription	HSMM	muscle
30	chr11:65852000-65856200	Weak transcription	Fetal Thymus	thymus
31	chr11:65852000-65857600	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr11:65852000-65858200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr11:65852000-65864800	Weak transcription	Lung	lung
34	chr11:65852000-65866800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr11:65852000-65867800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr11:65852000-65867800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr11:65852000-65874000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr11:65852200-65856000	Weak transcription	Small Intestine	intestine
39	chr11:65852200-65857600	Weak transcription	Left Ventricle	heart
40	chr11:65852200-65867600	Weak transcription	Right Ventricle	heart
41	chr11:65852200-65867800	Weak transcription	Thymus	Thymus
42	chr11:65852200-65871600	Weak transcription	Hela-S3	cervix
43	chr11:65852600-65868000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr11:65852800-65856000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr11:65852800-65856000	Weak transcription	Right Atrium	heart
46	chr11:65852800-65867400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr11:65852800-65867800	Weak transcription	Osteobl	bone
48	chr11:65853000-65867800	Weak transcription	Primary hematopoietic stem cells	blood
49	chr11:65853400-65871600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr11:65853600-65855800	Weak transcription	Fetal Heart	heart

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