Variant report

Variant	rs1193496
Chromosome Location	chr11:65537556-65537557
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:65486263..65488228-chr11:65537462..65540195,2	K562	blood:
2	chr11:65537505..65539315-chr11:65661843..65663867,2	MCF-7	breast:
3	chr11:65537232..65538956-chr11:65585286..65587865,2	MCF-7	breast:
4	chr11:65534494..65538893-chr11:65617709..65620478,3	K562	blood:
5	chr11:65536802..65537911-chr11:65585211..65586346,4	MCF-7	breast:
6	chr11:65492577..65494943-chr11:65537184..65539913,2	K562	blood:
7	chr11:65528026..65529884-chr11:65535933..65538399,2	K562	blood:
8	chr11:65536622..65537945-chr11:65585138..65586153,5	MCF-7	breast:
9	chr11:65536504..65538956-chr11:65583165..65585823,2	K562	blood:
10	chr11:65511937..65512528-chr11:65537362..65537959,2	MCF-7	breast:
11	chr11:65511963..65512619-chr11:65537012..65537973,4	MCF-7	breast:
12	chr11:65479037..65479823-chr11:65537297..65537846,2	MCF-7	breast:
13	chr11:65535765..65538772-chr11:65624238..65628078,4	MCF-7	breast:
14	chr11:65530310..65533560-chr11:65535934..65539165,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000172757	Chromatin interaction
ENSG00000172922	Chromatin interaction
ENSG00000172732	Chromatin interaction
ENSG00000214659	Chromatin interaction
ENSG00000172977	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10896041	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12146493	0.86[CHB][hapmap];0.90[CHD][hapmap];0.86[YRI][hapmap];0.87[ASN][1000 genomes]
rs12293022	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12801731	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2508301	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2508303	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs478304	0.93[EUR][1000 genomes]
rs495961	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs498354	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs502468	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs509206	0.93[EUR][1000 genomes]
rs522800	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs537786	1.00[CEU][hapmap];0.94[GIH][hapmap];0.98[TSI][hapmap];0.93[EUR][1000 genomes]
rs546202	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs570954	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs574483	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs603326	0.86[CHB][hapmap];0.80[ASN][1000 genomes]
rs603645	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs610037	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs614771	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61895666	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61895677	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs669742	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][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	nsv897718	chr11:65140209-65577516	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1003 gene(s)	inside rSNPs	diseases
2	nsv897736	chr11:65335705-65676516	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	227 gene(s)	inside rSNPs	diseases
3	nsv430401	chr11:65419324-65788024	Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	224 gene(s)	inside rSNPs	diseases
4	nsv897758	chr11:65490756-65564035	Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1193496	MAP3K11	cis	parietal	SCAN
rs1193496	RNASEH2C	cis	parietal	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65532400-65542200	Weak transcription	A549	lung
2	chr11:65532400-65542600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr11:65532600-65544000	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr11:65533000-65538000	Weak transcription	HepG2	liver
5	chr11:65533000-65542000	Weak transcription	Fetal Intestine Small	intestine
6	chr11:65533600-65543600	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr11:65534200-65544600	Weak transcription	Osteobl	bone
8	chr11:65534400-65542200	Enhancers	Placenta	Placenta
9	chr11:65534400-65542200	Weak transcription	NHDF-Ad	bronchial
10	chr11:65534400-65543800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr11:65536000-65542200	Weak transcription	Hela-S3	cervix
12	chr11:65536400-65541400	Enhancers	Primary neutrophils fromperipheralblood	blood
13	chr11:65536800-65537600	Enhancers	Primary hematopoietic stem cells	blood
14	chr11:65536800-65537800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr11:65536800-65537800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr11:65536800-65537800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr11:65536800-65537800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
18	chr11:65537000-65537600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr11:65537000-65538800	Enhancers	Primary B cells from cord blood	blood
20	chr11:65537000-65543800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr11:65537200-65537600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr11:65537200-65537600	Enhancers	HMEC	breast
23	chr11:65537200-65537800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr11:65537200-65538800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr11:65537400-65537800	Enhancers	K562	blood
26	chr11:65537400-65539000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr11:65537400-65542400	Weak transcription	Adipose Nuclei	Adipose
28	chr11:65537400-65542800	Weak transcription	Duodenum Mucosa	Duodenum
29	chr11:65537400-65543000	Weak transcription	Primary T cells from cord blood	blood
30	chr11:65537400-65544200	Weak transcription	NHLF	lung
31	chr11:65537400-65544400	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr11:65537400-65544400	Weak transcription	Dnd41	blood
33	chr11:65537400-65544600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr11:65537400-65544600	Weak transcription	Colon Smooth Muscle	Colon
35	chr11:65537400-65544600	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr11:65537400-65544800	Weak transcription	Brain Hippocampus Middle	brain
37	chr11:65537400-65545200	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr11:65537400-65546600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr11:65537400-65546600	Weak transcription	Rectal Smooth Muscle	rectum

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