Variant report

Variant	rs3808080
Chromosome Location	chr7:127575665-127575666
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:127568808..127571707-chr7:127574376..127576396,4	K562	blood:
2	chr7:127568481..127572943-chr7:127573201..127576396,5	K562	blood:
3	chr7:127574596..127577312-chr7:127578252..127580696,2	K562	blood:

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10226394	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10246505	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10265516	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10280863	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1035295	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11773160	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3757764	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3757768	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3808081	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3808083	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3808089	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4473953	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes]
rs57103099	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6960004	1.00[ASW][hapmap];0.91[LWK][hapmap];1.00[YRI][hapmap]
rs6965698	0.88[EUR][1000 genomes]
rs6968751	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs6969353	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6976887	0.82[EUR][1000 genomes]
rs7783102	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7786786	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022385	chr7:127246656-127971194	Weak transcription Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv539120	chr7:127246656-127971194	Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv1016143	chr7:127251359-127726762	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv526535	chr7:127445594-127623840	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1024743	chr7:127498695-127670004	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3808080	C7orf54	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:127562200-127589800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr7:127567600-127581400	Strong transcription	K562	blood
3	chr7:127567800-127577200	Weak transcription	Brain Hippocampus Middle	brain
4	chr7:127568000-127576200	Strong transcription	NHEK	skin
5	chr7:127568200-127577200	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr7:127568200-127583400	Weak transcription	Fetal Heart	heart
7	chr7:127568200-127594000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr7:127568600-127577000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr7:127569000-127576600	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr7:127569800-127615600	Weak transcription	Colonic Mucosa	Colon
11	chr7:127570000-127577200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr7:127570000-127577400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr7:127570000-127577400	Weak transcription	Brain Angular Gyrus	brain
14	chr7:127570000-127583800	Weak transcription	Psoas Muscle	Psoas
15	chr7:127570000-127585800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr7:127570000-127591400	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr7:127570200-127577200	Weak transcription	Colon Smooth Muscle	Colon
18	chr7:127570600-127576000	Weak transcription	Right Atrium	heart
19	chr7:127570600-127576000	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr7:127570600-127584600	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr7:127570600-127615600	Weak transcription	Small Intestine	intestine
22	chr7:127570600-127615800	Weak transcription	Esophagus	oesophagus
23	chr7:127570600-127616400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr7:127570800-127577800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr7:127570800-127583600	Weak transcription	Lung	lung
26	chr7:127570800-127589200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr7:127570800-127599600	Weak transcription	Stomach Smooth Muscle	stomach
28	chr7:127570800-127618200	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr7:127571000-127615600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr7:127571000-127615800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr7:127571200-127577200	Weak transcription	NHDF-Ad	bronchial
32	chr7:127571400-127578000	Weak transcription	NHLF	lung
33	chr7:127571400-127583600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr7:127571400-127589800	Weak transcription	Fetal Stomach	stomach
35	chr7:127571400-127617800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr7:127571600-127578400	Weak transcription	HMEC	breast
37	chr7:127571600-127582000	Weak transcription	Hela-S3	cervix
38	chr7:127571600-127582600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr7:127571600-127583600	Weak transcription	Right Ventricle	heart
40	chr7:127571600-127584800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr7:127571600-127594400	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr7:127571600-127618000	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr7:127571800-127577600	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr7:127571800-127577800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr7:127571800-127579800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr7:127571800-127583000	Weak transcription	Thymus	Thymus
47	chr7:127571800-127583600	Weak transcription	Brain Substantia Nigra	brain
48	chr7:127571800-127584000	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr7:127571800-127602800	Weak transcription	Aorta	Aorta
50	chr7:127572000-127576200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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