Variant report

Variant	rs668223
Chromosome Location	chr18:11990898-11990899
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:11978630..11983643-chr18:11987662..11991726,6	MCF-7	breast:
2	chr18:11949879..11951567-chr18:11988401..11991255,2	K562	blood:
3	chr18:11980570..11987752-chr18:11988318..11993643,9	K562	blood:

Variant related genes	Relation type
ENSG00000141401	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs3859296	0.95[CHB][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs58393627	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs588257	0.95[CHB][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs589247	0.95[CEU][hapmap];0.90[CHB][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs590100	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs590277	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs591061	0.90[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs592577	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs604962	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs605047	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs605636	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs605964	0.95[ASN][1000 genomes]
rs606020	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs606105	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs606370	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs606478	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs607200	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs622061	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs622246	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs636173	0.81[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs636300	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs638063	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs638125	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs644710	0.85[JPT][hapmap]
rs649396	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs649713	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs650727	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs655790	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs666521	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs667798	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs669838	0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs682271	0.91[ASN][1000 genomes]
rs683190	0.91[ASN][1000 genomes]
rs684680	0.95[CHB][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs9973072	0.81[CHB][hapmap];0.94[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055453	chr18:11776790-12110135	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv543654	chr18:11776790-12110135	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	esv2758470	chr18:11897023-12076102	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	esv2758713	chr18:11897023-12076102	Flanking Active TSS Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
5	nsv909384	chr18:11907374-12101109	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
6	nsv909386	chr18:11938102-12095950	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
7	nsv909388	chr18:11987988-12141372	Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	nsv909389	chr18:11987988-12141625	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
9	nsv909390	chr18:11987988-12155371	Active TSS Genic enhancers Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	nsv528699	chr18:11989416-12029857	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv909391	chr18:11989416-12146408	Active TSS Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
12	nsv909392	chr18:11989416-12146698	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:11982400-12005000	Weak transcription	Aorta	Aorta
2	chr18:11982600-11995600	Weak transcription	Primary T cells from cord blood	blood
3	chr18:11982600-11995800	Weak transcription	Thymus	Thymus
4	chr18:11982600-12028600	Weak transcription	Small Intestine	intestine
5	chr18:11983400-11994000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr18:11984200-11993600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr18:11984200-11994600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr18:11984400-11993400	Weak transcription	Lung	lung
9	chr18:11984400-11994200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr18:11984400-11994200	Weak transcription	NHEK	skin
11	chr18:11984400-11995000	Weak transcription	GM12878-XiMat	blood
12	chr18:11985200-11991200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr18:11986000-11995600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr18:11986400-11994600	Weak transcription	Liver	Liver
15	chr18:11986800-11992800	Enhancers	Fetal Muscle Trunk	muscle
16	chr18:11987200-11994800	Weak transcription	Right Atrium	heart
17	chr18:11987400-11991200	Enhancers	Fetal Lung	lung
18	chr18:11987600-11992400	Enhancers	Fetal Muscle Leg	muscle
19	chr18:11987800-11991400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr18:11988000-11991800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr18:11988000-11995600	Weak transcription	K562	blood
22	chr18:11988200-11991600	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr18:11988400-11991600	Enhancers	Esophagus	oesophagus
24	chr18:11988400-11991600	Enhancers	Psoas Muscle	Psoas
25	chr18:11988600-11991800	Enhancers	HUES6 Cell Line	embryonic stem cell
26	chr18:11988600-11995200	Weak transcription	Primary hematopoietic stem cells	blood
27	chr18:11988800-11991000	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr18:11988800-11991600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr18:11988800-11994200	Weak transcription	Adipose Nuclei	Adipose
30	chr18:11989000-11991200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr18:11989000-11991400	Genic enhancers	Fetal Stomach	stomach
32	chr18:11989000-11992400	Enhancers	Right Ventricle	heart
33	chr18:11989200-11991000	Enhancers	Stomach Smooth Muscle	stomach
34	chr18:11989200-11991200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr18:11989200-11991400	Enhancers	H1 Cell Line	embryonic stem cell
36	chr18:11989200-11991400	Genic enhancers	Placenta	Placenta
37	chr18:11989400-11991000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr18:11989400-11994400	Enhancers	HepG2	liver
39	chr18:11989400-11994600	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr18:11989600-11991000	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr18:11989600-11991000	Weak transcription	HSMMtube	muscle
42	chr18:11989600-11992400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr18:11989600-11996400	Enhancers	Pancreas	Pancrea
44	chr18:11989800-11991400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr18:11989800-11991600	Enhancers	Gastric	stomach
46	chr18:11989800-11992200	Weak transcription	Spleen	Spleen
47	chr18:11989800-11992800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr18:11989800-11993400	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr18:11989800-11994600	Weak transcription	Left Ventricle	heart
50	chr18:11990000-11991000	Enhancers	Cortex derived primary cultured neurospheres	brain

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