Variant report

Variant	rs62088908
Chromosome Location	chr18:9610552-9610553
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUN	chr18:9608123-9610557	K562	blood:	n/a	chr18:9610354-9610364 chr18:9608533-9608546 chr18:9610212-9610224 chr18:9608537-9608546

No.	Distal block	Cell Line	Cell type
1	chr18:9610312..9611854-chr18:9611926..9614343,2	MCF-7	breast:
2	chr18:9598014..9601741-chr18:9607589..9612497,6	MCF-7	breast:
3	chr18:9608061..9610764-chr18:9617117..9619483,2	MCF-7	breast:
4	chr18:9595087..9597869-chr18:9607007..9610720,3	MCF-7	breast:
5	chr18:9610247..9612763-chr18:9683592..9685519,2	K562	blood:

Variant related genes	Relation type
ENSG00000263627	TF binding region
ENSG00000212572	Chromatin interaction
ENSG00000154845	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1036930	0.86[AFR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11081487	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12327541	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16955297	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1869737	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1869738	0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1869739	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2028657	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2840354	0.81[ASN][1000 genomes]
rs55841197	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56883068	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57539299	0.81[ASN][1000 genomes]
rs58800301	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58982927	0.81[ASN][1000 genomes]
rs60290408	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61275183	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62087427	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62087456	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62088860	0.86[AFR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62088870	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62088872	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62088873	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62088875	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62088876	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62088880	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62088881	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62088884	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62088885	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62088904	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62088906	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6506677	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7228280	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7231531	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7233308	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7233649	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7234355	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7235935	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7236274	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7237018	0.81[ASN][1000 genomes]
rs7238137	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7239083	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72945737	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs732698	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8096551	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[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	esv3693417	chr18:9512985-9693638	Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	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
3	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
4	nsv543644	chr18:9576145-9612516	Strong transcription Enhancers Genic enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:9551000-9612200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr18:9553800-9613600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr18:9588600-9612400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr18:9589000-9611000	Weak transcription	Lung	lung
5	chr18:9594200-9613600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr18:9595200-9612000	Weak transcription	Esophagus	oesophagus
7	chr18:9596000-9611000	Weak transcription	Gastric	stomach
8	chr18:9597200-9611000	Weak transcription	NH-A	brain
9	chr18:9597400-9613200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr18:9598000-9612600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr18:9601400-9610800	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr18:9601600-9610800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr18:9601800-9612200	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr18:9603200-9610800	Weak transcription	Placenta	Placenta
15	chr18:9603200-9611000	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr18:9603600-9611000	Weak transcription	Fetal Muscle Trunk	muscle
17	chr18:9603800-9611000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr18:9604200-9611000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr18:9604400-9610800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr18:9604400-9611000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr18:9604600-9610800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr18:9604600-9611000	Weak transcription	Primary B cells from cord blood	blood
23	chr18:9604600-9611000	Weak transcription	Spleen	Spleen
24	chr18:9604800-9612200	Weak transcription	Primary B cells from peripheral blood	blood
25	chr18:9604800-9612400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr18:9605000-9611200	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr18:9605200-9610800	Weak transcription	Fetal Intestine Large	intestine
28	chr18:9605600-9611600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr18:9606000-9611000	Weak transcription	Primary hematopoietic stem cells	blood
30	chr18:9606600-9611000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr18:9606600-9611000	Weak transcription	HSMMtube	muscle
32	chr18:9607200-9613400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr18:9607800-9610800	Weak transcription	Stomach Smooth Muscle	stomach
34	chr18:9608000-9611200	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr18:9608000-9611600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr18:9608200-9613600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr18:9608600-9611000	Weak transcription	Brain Anterior Caudate	brain
38	chr18:9608600-9611400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr18:9608800-9611000	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr18:9609000-9612200	Weak transcription	Fetal Kidney	kidney
41	chr18:9609000-9612400	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr18:9609200-9611000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr18:9609200-9611000	Weak transcription	Adipose Nuclei	Adipose
44	chr18:9609200-9612200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr18:9609400-9610800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr18:9609400-9611000	Weak transcription	Brain Hippocampus Middle	brain
47	chr18:9609400-9611000	Weak transcription	Colon Smooth Muscle	Colon
48	chr18:9609400-9611000	Weak transcription	Fetal Brain Female	brain
49	chr18:9609400-9612000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr18:9609400-9612000	Weak transcription	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links