Variant report

Variant	rs16977227
Chromosome Location	chr18:12480695-12480696
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:12480204..12483601-chr18:12657660..12659275,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000215527	Chromatin interaction
ENSG00000128789	Chromatin interaction
ENSG00000134278	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11663358	0.86[AFR][1000 genomes]
rs11664219	0.87[CEU][hapmap];1.00[YRI][hapmap]
rs11664232	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11665415	0.87[CEU][hapmap];0.84[YRI][hapmap]
rs11665542	0.87[CEU][hapmap];0.91[YRI][hapmap]
rs16973057	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16977205	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16977214	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1893236	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2040197	0.82[AFR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3887990	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4566245	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4797687	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4797689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4797693	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56723469	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58500351	0.82[AFR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60563648	0.81[AFR][1000 genomes]
rs73403752	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73403754	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73403761	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73403763	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73405602	0.86[AFR][1000 genomes]
rs73949246	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9959201	1.00[CEU][hapmap];0.91[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063125	chr18:12046892-12918251	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
2	nsv491873	chr18:12159445-12739784	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
3	nsv909400	chr18:12201374-12585545	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	esv2758471	chr18:12240681-12499525	Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
5	esv2758714	chr18:12240681-12499525	Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
6	nsv576496	chr18:12247872-12490502	Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
7	nsv1060808	chr18:12302792-12514417	Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
8	esv3528039	chr18:12396582-12851293	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
9	esv3528041	chr18:12396641-12851245	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
10	nsv2208	chr18:12472999-12518189	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
11	nsv523743	chr18:12474505-12742809	Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12453400-12484400	Weak transcription	Hela-S3	cervix
2	chr18:12460200-12516600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr18:12461200-12481200	Weak transcription	Primary hematopoietic stem cells	blood
4	chr18:12461400-12495400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr18:12463400-12491800	Weak transcription	Psoas Muscle	Psoas
6	chr18:12465000-12491400	Weak transcription	NHDF-Ad	bronchial
7	chr18:12465600-12500800	Weak transcription	Fetal Intestine Large	intestine
8	chr18:12472600-12495200	Weak transcription	Colonic Mucosa	Colon
9	chr18:12477000-12481000	Strong transcription	HSMM	muscle
10	chr18:12477000-12481200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr18:12477000-12482200	Strong transcription	HSMMtube	muscle
12	chr18:12477200-12490800	Weak transcription	K562	blood
13	chr18:12477400-12480800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr18:12478400-12485400	Weak transcription	Fetal Thymus	thymus
15	chr18:12478400-12512600	Weak transcription	Fetal Intestine Small	intestine
16	chr18:12478600-12496000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr18:12478600-12498400	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr18:12478600-12506400	Weak transcription	Right Ventricle	heart
19	chr18:12478600-12510800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr18:12478800-12481600	Weak transcription	Fetal Heart	heart
21	chr18:12478800-12485200	Weak transcription	HUVEC	blood vessel
22	chr18:12478800-12485400	Weak transcription	HMEC	breast
23	chr18:12478800-12485600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr18:12478800-12485600	Weak transcription	NHEK	skin
25	chr18:12478800-12485800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr18:12478800-12488000	Weak transcription	Left Ventricle	heart
27	chr18:12478800-12490800	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr18:12478800-12491200	Weak transcription	Liver	Liver
29	chr18:12478800-12491400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr18:12478800-12491400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr18:12478800-12491400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr18:12478800-12491400	Weak transcription	Brain Anterior Caudate	brain
33	chr18:12478800-12491400	Weak transcription	Fetal Brain Female	brain
34	chr18:12478800-12491400	Weak transcription	Fetal Lung	lung
35	chr18:12478800-12491400	Weak transcription	HepG2	liver
36	chr18:12478800-12491400	Weak transcription	Osteobl	bone
37	chr18:12478800-12491600	Weak transcription	Brain Cingulate Gyrus	brain
38	chr18:12478800-12491600	Weak transcription	Brain Hippocampus Middle	brain
39	chr18:12478800-12491600	Weak transcription	Colon Smooth Muscle	Colon
40	chr18:12478800-12491600	Weak transcription	Esophagus	oesophagus
41	chr18:12478800-12491600	Weak transcription	Fetal Kidney	kidney
42	chr18:12478800-12491600	Weak transcription	Fetal Muscle Trunk	muscle
43	chr18:12478800-12491600	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr18:12478800-12491600	Weak transcription	Spleen	Spleen
45	chr18:12478800-12492000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr18:12478800-12492800	Weak transcription	Fetal Brain Male	brain
47	chr18:12478800-12497400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr18:12478800-12499600	Weak transcription	NHLF	lung
49	chr18:12478800-12504800	Weak transcription	Gastric	stomach
50	chr18:12478800-12505800	Weak transcription	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links