Variant report

Variant	rs17080108
Chromosome Location	chr6:151006643-151006644
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:151004338..151007034-chr6:151012043..151014103,2	MCF-7	breast:
2	chr6:151005271..151008219-chr6:151020756..151022583,2	K562	blood:
3	chr6:150997606..151001974-chr6:151004328..151007109,4	K562	blood:

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs12661140	0.86[JPT][hapmap]
rs12664686	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17080073	1.00[CEU][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17080089	0.86[JPT][hapmap];0.84[YRI][hapmap];0.90[AFR][1000 genomes]
rs17080091	0.84[YRI][hapmap];0.89[AFR][1000 genomes]
rs17080093	0.86[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs2345745	0.93[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4036092	0.82[EUR][1000 genomes]
rs4869926	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4869927	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4869928	0.81[CEU][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4869929	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4869930	0.93[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4869931	0.93[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55646755	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs57139556	0.90[AFR][1000 genomes]
rs58824807	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59466561	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62434122	0.88[AFR][1000 genomes]
rs62434123	0.90[AFR][1000 genomes]
rs62434124	0.88[AFR][1000 genomes]
rs6899782	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6908127	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6929743	0.93[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73010188	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9478775	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9478780	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9478783	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9480514	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9480526	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9480528	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9480529	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9480530	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9480531	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9480533	0.86[CEU][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9885650	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9885699	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9885836	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]

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	nsv886772	chr6:150743364-151024280	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1030326	chr6:150967665-151641372	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS 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	25 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:150980600-151008800	Weak transcription	Gastric	stomach
2	chr6:150980800-151014800	Weak transcription	Pancreas	Pancrea
3	chr6:150989400-151007800	Weak transcription	Ovary	ovary
4	chr6:150990600-151008800	Weak transcription	Rectal Smooth Muscle	rectum
5	chr6:150990600-151016600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr6:150990800-151011800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:150995000-151008800	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr6:150995400-151008800	Weak transcription	Small Intestine	intestine
9	chr6:150996600-151008000	Weak transcription	Fetal Intestine Large	intestine
10	chr6:151000800-151010000	Enhancers	Primary B cells from peripheral blood	blood
11	chr6:151001600-151008200	Genic enhancers	Fetal Thymus	thymus
12	chr6:151002400-151007800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr6:151003000-151006800	Strong transcription	Fetal Stomach	stomach
14	chr6:151003400-151007400	Genic enhancers	Thymus	Thymus
15	chr6:151003600-151007600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr6:151003600-151011400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:151003800-151007400	Weak transcription	NHEK	skin
18	chr6:151003800-151015000	Weak transcription	Brain Substantia Nigra	brain
19	chr6:151004000-151007000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr6:151004000-151007000	Weak transcription	HMEC	breast
21	chr6:151004200-151007000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr6:151004200-151007000	Weak transcription	Fetal Kidney	kidney
23	chr6:151004800-151012000	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr6:151005000-151007000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr6:151005000-151017400	Weak transcription	Aorta	Aorta
26	chr6:151005200-151007400	Enhancers	HUVEC	blood vessel
27	chr6:151005400-151007200	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr6:151005800-151008000	Enhancers	Placenta	Placenta
29	chr6:151005800-151018400	Weak transcription	Psoas Muscle	Psoas
30	chr6:151006000-151006800	Enhancers	Esophagus	oesophagus
31	chr6:151006000-151006800	Enhancers	Rectal Mucosa Donor 29	rectum
32	chr6:151006000-151006800	Enhancers	Sigmoid Colon	Sigmoid Colon
33	chr6:151006000-151007400	Enhancers	Right Ventricle	heart
34	chr6:151006000-151008000	Enhancers	Left Ventricle	heart
35	chr6:151006000-151018400	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr6:151006200-151006800	Enhancers	Duodenum Mucosa	Duodenum
37	chr6:151006200-151007600	Weak transcription	Fetal Muscle Leg	muscle
38	chr6:151006400-151007600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr6:151006600-151006800	Flanking Active TSS	Adipose Nuclei	Adipose
40	chr6:151006600-151006800	ZNF genes & repeats	GM12878-XiMat	blood
41	chr6:151006600-151007000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr6:151006600-151007600	Weak transcription	Fetal Lung	lung
43	chr6:151006600-151007800	Weak transcription	Lung	lung
44	chr6:151006600-151007800	Weak transcription	Spleen	Spleen
45	chr6:151006600-151008000	Weak transcription	Stomach Mucosa	stomach
46	chr6:151006600-151008400	Weak transcription	Liver	Liver
47	chr6:151006600-151011400	Enhancers	Primary B cells from cord blood	blood
48	chr6:151006600-151011800	Weak transcription	Primary hematopoietic stem cells	blood
49	chr6:151006600-151011800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr6:151006600-151014600	Weak transcription	Right Atrium	heart

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