Variant report

Variant	rs9946546
Chromosome Location	chr18:9753599-9753600
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:9707138..9711181-chr18:9753549..9757373,4	MCF-7	breast:
2	chr18:9743133..9745591-chr18:9751999..9754524,3	K562	blood:
3	chr18:9752235..9755136-chr18:9913982..9916846,2	K562	blood:

Variant related genes	Relation type
ENSG00000101558	Chromatin interaction
ENSG00000168461	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs16955541	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4798846	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4798848	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4798849	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62081160	0.80[EUR][1000 genomes]
rs6506696	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8085958	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8086019	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8086030	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8086174	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8091737	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8092949	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8093100	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8093221	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8099036	0.81[EUR][1000 genomes]
rs9951171	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9958317	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9966247	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]

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	nsv458024	chr18:9558240-9828448	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv576448	chr18:9558240-9828448	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv469897	chr18:9674498-9870517	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv482461	chr18:9674498-9870517	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv1064807	chr18:9695356-9770358	Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv9606	chr18:9743017-9755287	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
7	esv2757669	chr18:9743326-9753992	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	esv2758712	chr18:9743326-9753992	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
9	nsv828177	chr18:9743875-9754292	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
10	esv1821203	chr18:9747676-9757934	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
11	esv1796843	chr18:9749799-9757934	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
12	esv1796789	chr18:9749957-9757734	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:9742800-9754400	Weak transcription	Right Ventricle	heart
2	chr18:9743000-9756200	Weak transcription	Rectal Smooth Muscle	rectum
3	chr18:9743400-9754800	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr18:9743600-9755400	Weak transcription	Fetal Stomach	stomach
5	chr18:9744000-9754800	Weak transcription	Aorta	Aorta
6	chr18:9744000-9755400	Weak transcription	Lung	lung
7	chr18:9744000-9755600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr18:9744000-9757600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr18:9744200-9754800	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr18:9744400-9753600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr18:9744400-9753600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr18:9744400-9755200	Weak transcription	K562	blood
13	chr18:9744400-9755400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr18:9744400-9757000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr18:9744400-9757000	Weak transcription	HSMMtube	muscle
16	chr18:9744400-9757200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr18:9744800-9753600	Weak transcription	A549	lung
18	chr18:9747800-9755400	Weak transcription	Colon Smooth Muscle	Colon
19	chr18:9748200-9759600	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr18:9749000-9755000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr18:9750200-9771400	Weak transcription	Brain Angular Gyrus	brain
22	chr18:9750400-9756800	Weak transcription	Brain Hippocampus Middle	brain
23	chr18:9750600-9755400	Weak transcription	Spleen	Spleen
24	chr18:9750800-9758200	Weak transcription	NHLF	lung
25	chr18:9750800-9764000	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr18:9751000-9757600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr18:9751000-9757800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr18:9751000-9760600	Enhancers	Monocytes-CD14+_RO01746	blood
29	chr18:9751000-9762200	Enhancers	Primary neutrophils fromperipheralblood	blood
30	chr18:9751400-9756400	Weak transcription	Primary B cells from cord blood	blood
31	chr18:9751600-9756600	Weak transcription	Stomach Smooth Muscle	stomach
32	chr18:9751600-9757000	Weak transcription	Brain Substantia Nigra	brain
33	chr18:9751800-9755600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr18:9751800-9758200	Weak transcription	Brain Anterior Caudate	brain
35	chr18:9752000-9755200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr18:9752000-9755200	Weak transcription	NH-A	brain
37	chr18:9752000-9757600	Weak transcription	Pancreas	Pancrea
38	chr18:9752200-9754000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr18:9752200-9755200	Weak transcription	Fetal Muscle Leg	muscle
40	chr18:9752200-9755400	Weak transcription	Primary hematopoietic stem cells	blood
41	chr18:9752200-9766000	Weak transcription	Ovary	ovary
42	chr18:9752400-9754800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr18:9752400-9755400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr18:9752600-9757000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr18:9753000-9754200	Enhancers	Placenta	Placenta
46	chr18:9753000-9755200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr18:9753200-9753800	Flanking Active TSS	Hela-S3	cervix
48	chr18:9753200-9754200	Enhancers	NHEK	skin
49	chr18:9753200-9755400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr18:9753200-9756400	Enhancers	Osteobl	bone

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