Variant report

Variant	rs16899123
Chromosome Location	chr6:166955134-166955135
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11961434	0.81[AMR][1000 genomes]
rs11963921	0.81[AMR][1000 genomes]
rs11964118	0.89[AMR][1000 genomes]
rs11964417	0.81[AMR][1000 genomes]
rs11969154	0.89[AMR][1000 genomes]
rs11969174	0.89[AMR][1000 genomes]
rs11969176	0.89[AMR][1000 genomes]
rs16899080	0.81[AMR][1000 genomes]
rs16899084	0.81[AMR][1000 genomes]
rs16899091	0.81[AMR][1000 genomes]
rs16899093	0.90[AMR][1000 genomes]
rs16899098	0.93[YRI][hapmap];0.90[AMR][1000 genomes]
rs16899101	0.90[AMR][1000 genomes]
rs16899105	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs16899126	0.89[AMR][1000 genomes]
rs16899129	0.89[AMR][1000 genomes]
rs16899150	0.89[AMR][1000 genomes]
rs16899151	0.89[AMR][1000 genomes]
rs16899157	0.89[AMR][1000 genomes]
rs3778414	0.81[AMR][1000 genomes]
rs4490642	0.81[AMR][1000 genomes]
rs57647994	0.89[AMR][1000 genomes]
rs58004496	0.90[AMR][1000 genomes]
rs59766415	0.90[AMR][1000 genomes]
rs59815364	0.81[AMR][1000 genomes]
rs60005152	0.89[AMR][1000 genomes]
rs61045375	0.89[AMR][1000 genomes]
rs6905167	0.81[AMR][1000 genomes]
rs6909530	0.90[AMR][1000 genomes]
rs6936351	0.81[AMR][1000 genomes]
rs73255153	0.81[AMR][1000 genomes]
rs73255159	0.81[AMR][1000 genomes]
rs73255165	0.81[AMR][1000 genomes]
rs73255166	0.81[AMR][1000 genomes]
rs73255201	0.89[AMR][1000 genomes]
rs73257211	0.89[AMR][1000 genomes]
rs73257221	0.89[AMR][1000 genomes]
rs73257223	0.89[AMR][1000 genomes]
rs73257240	0.89[AMR][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	esv3490076	chr6:166727901-167306743	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
2	esv3490077	chr6:166727901-167306743	Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
3	nsv886941	chr6:166907173-166996991	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:166929600-166955600	Weak transcription	HMEC	breast
2	chr6:166930400-166957800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr6:166935400-166966400	Weak transcription	NH-A	brain
4	chr6:166938200-166955800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr6:166941400-166955600	Weak transcription	Colon Smooth Muscle	Colon
6	chr6:166944600-166955600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr6:166944600-166957200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr6:166944600-166958600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr6:166947400-166969400	Weak transcription	Aorta	Aorta
10	chr6:166949800-166955800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr6:166949800-166955800	Weak transcription	NHLF	lung
12	chr6:166949800-166956800	Weak transcription	Right Ventricle	heart
13	chr6:166949800-166964800	Weak transcription	Fetal Intestine Small	intestine
14	chr6:166950000-166955400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr6:166950200-166960600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr6:166950800-166958600	Weak transcription	NHDF-Ad	bronchial
17	chr6:166951600-166955600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr6:166951800-166959000	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr6:166952000-166955400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr6:166952000-166955800	Weak transcription	HUVEC	blood vessel
21	chr6:166952000-166957000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr6:166952400-166957200	Weak transcription	Fetal Brain Male	brain
23	chr6:166952400-166969000	Weak transcription	Psoas Muscle	Psoas
24	chr6:166952800-166955400	Weak transcription	Fetal Stomach	stomach
25	chr6:166953000-166956200	Enhancers	HUES6 Cell Line	embryonic stem cell
26	chr6:166953000-166956400	Enhancers	iPS-18 Cell Line	embryonic stem cell
27	chr6:166953000-166957800	Enhancers	iPS-20b Cell Line	embryonic stem cell
28	chr6:166953000-166959000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr6:166953200-166956600	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr6:166953400-166955200	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr6:166953400-166955400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
32	chr6:166953400-166955600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr6:166953400-166955800	Enhancers	Brain Hippocampus Middle	brain
34	chr6:166953400-166957200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr6:166953400-166957600	Enhancers	H1 Cell Line	embryonic stem cell
36	chr6:166953400-166964600	Weak transcription	Primary T cells from cord blood	blood
37	chr6:166953400-166967400	Weak transcription	Fetal Lung	lung
38	chr6:166954000-166955200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
39	chr6:166954000-166956000	Flanking Active TSS	GM12878-XiMat	blood
40	chr6:166954000-166959000	Enhancers	Fetal Muscle Leg	muscle
41	chr6:166954200-166955200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr6:166954200-166955200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
43	chr6:166954200-166955200	Enhancers	Esophagus	oesophagus
44	chr6:166954200-166956000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr6:166954200-166956000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
46	chr6:166954200-166956000	Enhancers	Fetal Thymus	thymus
47	chr6:166954200-166958200	Enhancers	Fetal Muscle Trunk	muscle
48	chr6:166954200-166965000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr6:166954400-166955200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
50	chr6:166954400-166955200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood

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