Variant report

Variant	rs16899930
Chromosome Location	chr8:125666588-125666589
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:125665485..125668250-chr8:125822929..125824951,2	K562	blood:
2	chr8:125665987..125668310-chr8:125675466..125678382,3	K562	blood:
3	chr8:125664797..125667579-chr8:125686939..125689871,2	K562	blood:
4	chr8:125658978..125663524-chr8:125664698..125669211,7	MCF-7	breast:
5	chr8:125665322..125667736-chr8:126082032..126083680,2	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10216358	0.87[CEU][hapmap];1.00[CHB][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10505447	1.00[JPT][hapmap]
rs16899921	0.87[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16899925	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16899927	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16899928	1.00[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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16899933	1.00[JPT][hapmap]
rs16899942	1.00[JPT][hapmap]
rs17374540	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2008250	1.00[JPT][hapmap]
rs28576363	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28703083	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28733819	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57660221	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6989891	1.00[JPT][hapmap]
rs7010266	0.87[CEU][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7813190	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7835359	1.00[JPT][hapmap]
rs7838755	1.00[JPT][hapmap]
rs7840201	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1027585	chr8:125627924-125707738	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
2	nsv891434	chr8:125630655-126324432	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
3	nsv1016502	chr8:125657664-125845074	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16899930	CAPS	trans	brain	seeQTL

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:125650000-125666800	Weak transcription	Esophagus	oesophagus
2	chr8:125654000-125666800	Weak transcription	Fetal Muscle Leg	muscle
3	chr8:125655000-125666800	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr8:125655000-125672200	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr8:125655200-125667400	Weak transcription	Fetal Muscle Trunk	muscle
6	chr8:125655200-125667400	Weak transcription	NHDF-Ad	bronchial
7	chr8:125657000-125667400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr8:125657000-125667600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr8:125658600-125667600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr8:125661600-125667200	Weak transcription	Fetal Intestine Large	intestine
11	chr8:125662000-125666800	Weak transcription	Brain Cingulate Gyrus	brain
12	chr8:125662000-125666800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr8:125662000-125678400	Weak transcription	Fetal Brain Female	brain
14	chr8:125662200-125667000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr8:125662200-125667600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr8:125662200-125667800	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr8:125662600-125668600	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr8:125662800-125666800	Weak transcription	Brain Substantia Nigra	brain
19	chr8:125662800-125667400	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr8:125663000-125668600	Weak transcription	HUVEC	blood vessel
21	chr8:125663800-125667400	Weak transcription	Brain Hippocampus Middle	brain
22	chr8:125663800-125672200	Weak transcription	Fetal Stomach	stomach
23	chr8:125664000-125666600	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr8:125664000-125666800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr8:125664000-125666800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr8:125664000-125667400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr8:125664200-125666800	Genic enhancers	Primary B cells from peripheral blood	blood
28	chr8:125664200-125666800	Weak transcription	Thymus	Thymus
29	chr8:125664200-125667200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr8:125664200-125667200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr8:125664200-125667200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr8:125664200-125672200	Weak transcription	HSMMtube	muscle
33	chr8:125664400-125667400	Enhancers	K562	blood
34	chr8:125664400-125669800	Weak transcription	Placenta	Placenta
35	chr8:125665200-125667000	Genic enhancers	Primary B cells from cord blood	blood
36	chr8:125665400-125668000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr8:125665600-125666800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr8:125666000-125666600	Genic enhancers	Brain Germinal Matrix	brain
39	chr8:125666000-125667000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr8:125666000-125667000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr8:125666000-125667200	Genic enhancers	HepG2	liver
42	chr8:125666000-125668200	Enhancers	Fetal Thymus	thymus
43	chr8:125666000-125668400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr8:125666000-125669000	Enhancers	Skeletal Muscle Male	skeletal muscle
45	chr8:125666000-125669400	Enhancers	Fetal Kidney	kidney
46	chr8:125666200-125667000	Enhancers	Brain Anterior Caudate	brain
47	chr8:125666200-125667000	Enhancers	Pancreatic Islets	Pancreatic Islet
48	chr8:125666200-125667200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr8:125666200-125667400	Enhancers	Lung	lung
50	chr8:125666200-125667800	Enhancers	Gastric	stomach

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