Variant report

Variant	rs11660889
Chromosome Location	chr18:9177297-9177298
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:9175098..9178757-chr18:9180431..9183034,3	K562	blood:
2	chr18:9177075..9179067-chr18:9181095..9183827,3	K562	blood:

Variant related genes	Relation type
ENSG00000101745	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1034486	0.90[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1046491	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10502390	0.90[CEU][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs10853373	0.88[AMR][1000 genomes]
rs11081459	0.89[CEU][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs11081463	0.89[CEU][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs11081469	0.89[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11661901	0.88[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11661921	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11663175	0.89[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11663949	0.90[CEU][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11872176	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11872481	0.90[CEU][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes]
rs11875086	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11876775	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11876821	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11877843	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12454025	1.00[YRI][hapmap];0.90[AMR][1000 genomes]
rs12454497	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12454908	0.90[AMR][1000 genomes]
rs12454936	0.90[AMR][1000 genomes]
rs12455304	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12457266	0.93[AMR][1000 genomes]
rs12457429	0.93[AMR][1000 genomes]
rs12956160	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12966444	0.86[YRI][hapmap];0.90[AMR][1000 genomes]
rs12966775	0.90[CEU][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes]
rs12968060	0.90[CEU][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes]
rs34322928	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35002591	0.84[AMR][1000 genomes]
rs35587943	0.84[AMR][1000 genomes]
rs35774167	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35849084	0.93[AMR][1000 genomes]
rs41274300	0.90[AMR][1000 genomes]
rs62085924	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62085926	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62085927	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6506641	0.84[AMR][1000 genomes]
rs6506647	0.90[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs71362073	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7226632	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7229685	0.80[CEU][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8085549	0.89[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8085669	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8086362	1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8089577	1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8090297	0.90[AMR][1000 genomes]
rs8095601	0.90[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916373	chr18:9026803-9592201	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv431971	chr18:9081185-9326852	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv1056258	chr18:9094498-9181498	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv909364	chr18:9114096-9186684	Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv543641	chr18:9120450-9181498	Genic enhancers Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv543642	chr18:9133164-9191739	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv1056407	chr18:9144345-9553764	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:9148400-9187200	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr18:9153600-9182400	Weak transcription	Liver	Liver
3	chr18:9153600-9185000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr18:9157400-9182400	Weak transcription	HepG2	liver
5	chr18:9162200-9187800	Weak transcription	Thymus	Thymus
6	chr18:9164400-9200600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr18:9165600-9183000	Weak transcription	Primary T cells from cord blood	blood
8	chr18:9165600-9195400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr18:9168400-9185600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr18:9170200-9181400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr18:9171600-9177800	Enhancers	Primary T helper naive cells from peripheral blood	blood
12	chr18:9171600-9180800	Weak transcription	NHDF-Ad	bronchial
13	chr18:9172000-9182200	Weak transcription	Fetal Lung	lung
14	chr18:9172000-9216200	Weak transcription	Fetal Brain Female	brain
15	chr18:9172200-9185000	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr18:9172400-9187000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr18:9172600-9182200	Weak transcription	Dnd41	blood
18	chr18:9173000-9208400	Weak transcription	NHLF	lung
19	chr18:9173200-9182000	Weak transcription	Fetal Intestine Large	intestine
20	chr18:9174000-9178400	Enhancers	Primary T killer memory cells from peripheral blood	blood
21	chr18:9174000-9182800	Weak transcription	Osteobl	bone
22	chr18:9174200-9191800	Weak transcription	Fetal Stomach	stomach
23	chr18:9174200-9192000	Weak transcription	HMEC	breast
24	chr18:9174400-9179200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr18:9174400-9180000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr18:9174400-9180800	Weak transcription	K562	blood
27	chr18:9174400-9181000	Weak transcription	NHEK	skin
28	chr18:9174400-9182800	Weak transcription	HSMM	muscle
29	chr18:9174400-9183800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr18:9174400-9184000	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr18:9174400-9191800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr18:9174600-9180800	Weak transcription	Brain Angular Gyrus	brain
33	chr18:9174600-9183000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr18:9174600-9183800	Weak transcription	Primary B cells from cord blood	blood
35	chr18:9174600-9184000	Weak transcription	Placenta	Placenta
36	chr18:9174600-9184400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr18:9174600-9184600	Weak transcription	Adipose Nuclei	Adipose
38	chr18:9174600-9185000	Weak transcription	Duodenum Mucosa	Duodenum
39	chr18:9174600-9188000	Weak transcription	Ovary	ovary
40	chr18:9174600-9188000	Weak transcription	HSMMtube	muscle
41	chr18:9174600-9188200	Weak transcription	Fetal Thymus	thymus
42	chr18:9174600-9233600	Weak transcription	Spleen	Spleen
43	chr18:9174800-9180000	Weak transcription	Brain Substantia Nigra	brain
44	chr18:9174800-9180200	Weak transcription	Brain Anterior Caudate	brain
45	chr18:9174800-9183200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr18:9174800-9184400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr18:9174800-9184600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr18:9174800-9184600	Weak transcription	Gastric	stomach
49	chr18:9174800-9187000	Weak transcription	Brain Cingulate Gyrus	brain
50	chr18:9174800-9187000	Weak transcription	Esophagus	oesophagus

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