Variant report

Variant	rs10659
Chromosome Location	chr6:110146497-110146498
allele	A/G
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	CTCF	chr6:110146380-110146530	Caco-2	colon:	n/a	n/a
2	CTCF	chr6:110146460-110146610	Caco-2	colon:	n/a	n/a
3	RAD21	chr6:110146275-110146577	H1-hESC	embryonic stem cell:	n/a	n/a
4	RAD21	chr6:110146407-110146504	H1-hESC	embryonic stem cell:	n/a	n/a
5	CTCF	chr6:110146426-110146516	MCF-7	breast:	n/a	n/a
6	CTCF	chr6:110146430-110146507	MCF-7	breast:	n/a	n/a
7	CTCF	chr6:110146426-110146532	Hela-S3	cervix:	n/a	n/a
8	CTCF	chr6:110146396-110146497	LNCaP	prostate:	n/a	n/a

Variant related genes	Relation type
ENSG00000232311	TF binding region

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs13437149	1.00[CEU][hapmap]
rs17070874	1.00[CEU][hapmap]
rs17070970	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17070972	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17070984	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2076929	1.00[CEU][hapmap]
rs2295835	1.00[CEU][hapmap]
rs2295836	1.00[CEU][hapmap]
rs34735897	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3823235	1.00[CEU][hapmap]
rs4512266	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58730628	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59180278	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60456575	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6568587	1.00[CEU][hapmap]
rs6917383	1.00[CEU][hapmap]
rs6933729	1.00[CEU][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6935696	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7356790	1.00[CEU][hapmap]
rs73762801	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73765003	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73765007	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73765009	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7742066	1.00[CEU][hapmap]
rs7744512	0.82[ASW][hapmap];1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7765916	1.00[CEU][hapmap]
rs7767805	1.00[CEU][hapmap]
rs9372226	1.00[CEU][hapmap]
rs9386835	1.00[CEU][hapmap]
rs9386842	1.00[CEU][hapmap]
rs9398214	1.00[CEU][hapmap]
rs9398215	1.00[CEU][hapmap]
rs9481003	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949475	chr6:109907936-110160501	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1019690	chr6:110102601-110360778	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:110082000-110152600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr6:110090400-110149200	Weak transcription	Fetal Intestine Large	intestine
3	chr6:110115800-110155800	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr6:110116200-110152000	Weak transcription	Colonic Mucosa	Colon
5	chr6:110117400-110148200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr6:110117600-110152000	Weak transcription	Fetal Muscle Trunk	muscle
7	chr6:110117600-110155400	Weak transcription	Rectal Smooth Muscle	rectum
8	chr6:110117600-110159200	Weak transcription	Pancreas	Pancrea
9	chr6:110118800-110149800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr6:110118800-110152400	Weak transcription	Duodenum Mucosa	Duodenum
11	chr6:110118800-110152400	Weak transcription	Thymus	Thymus
12	chr6:110121200-110148800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr6:110121200-110150600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr6:110121400-110147600	Weak transcription	NHLF	lung
15	chr6:110126600-110152400	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr6:110130000-110155800	Weak transcription	HSMMtube	muscle
17	chr6:110131800-110152400	Weak transcription	Esophagus	oesophagus
18	chr6:110132000-110149800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr6:110132400-110151800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr6:110134800-110155400	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr6:110135600-110155800	Weak transcription	Gastric	stomach
22	chr6:110136600-110149200	Weak transcription	Brain Hippocampus Middle	brain
23	chr6:110137000-110149200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr6:110137800-110155400	Weak transcription	Brain Angular Gyrus	brain
25	chr6:110137800-110155600	Weak transcription	Fetal Brain Female	brain
26	chr6:110138200-110154200	Weak transcription	Right Ventricle	heart
27	chr6:110138800-110155400	Weak transcription	Brain Germinal Matrix	brain
28	chr6:110139800-110154400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr6:110141400-110154400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr6:110142600-110146600	Enhancers	Primary neutrophils fromperipheralblood	blood
31	chr6:110142600-110155400	Weak transcription	Colon Smooth Muscle	Colon
32	chr6:110143000-110155200	Weak transcription	Fetal Lung	lung
33	chr6:110144200-110150800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr6:110144400-110147000	Strong transcription	Primary B cells from cord blood	blood
35	chr6:110144400-110149000	Strong transcription	Stomach Smooth Muscle	stomach
36	chr6:110144400-110150600	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr6:110144400-110151200	Strong transcription	Primary T cells from cord blood	blood
38	chr6:110144600-110148600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr6:110144800-110146600	Strong transcription	Spleen	Spleen
40	chr6:110144800-110147000	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr6:110144800-110148200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr6:110144800-110150800	Strong transcription	Primary B cells from peripheral blood	blood
43	chr6:110144800-110151200	Strong transcription	Adipose Nuclei	Adipose
44	chr6:110144800-110153400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr6:110145000-110146600	Strong transcription	Skeletal Muscle Male	skeletal muscle
46	chr6:110145000-110146800	Strong transcription	Aorta	Aorta
47	chr6:110145000-110148400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr6:110145000-110150800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr6:110145200-110146600	Strong transcription	Left Ventricle	heart
50	chr6:110145200-110155200	Weak transcription	Fetal Heart	heart

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