Variant report

Variant	rs16854900
Chromosome Location	chr1:179855400-179855401
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:179853596..179856683-chr1:179859981..179861933,3	MCF-7	breast:
2	chr1:179850478..179853234-chr1:179853885..179855815,2	MCF-7	breast:
3	chr1:179854286..179855981-chr1:179868215..179870330,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272906	Chromatin interaction
ENSG00000264916	Chromatin interaction
ENSG00000143337	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs16854717	1.00[TSI][hapmap]
rs57058804	1.00[EUR][1000 genomes]
rs60582916	1.00[EUR][1000 genomes]
rs73050384	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005808	chr1:179783922-179864710	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv1005051	chr1:179785643-179861950	Flanking Active TSS Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
3	nsv429936	chr1:179790343-180214343	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
4	nsv429947	chr1:179790518-179925104	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	esv1815608	chr1:179813499-180067988	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
6	nsv429958	chr1:179814306-179994628	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
7	nsv518936	chr1:179847402-179858333	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16854900	C17orf97	trans	lymphoblastoid	seeQTL

Chromatin state (count:132 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179852800-179858800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:179852800-179859800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:179852800-179860800	Weak transcription	Stomach Mucosa	stomach
4	chr1:179852800-179871200	Weak transcription	Spleen	Spleen
5	chr1:179853000-179855400	Weak transcription	Ovary	ovary
6	chr1:179853000-179857000	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr1:179853000-179858800	Weak transcription	Lung	lung
8	chr1:179853000-179884800	Weak transcription	Esophagus	oesophagus
9	chr1:179853000-179890400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr1:179853200-179855400	Weak transcription	Small Intestine	intestine
11	chr1:179853200-179855800	Enhancers	Rectal Smooth Muscle	rectum
12	chr1:179853200-179857000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr1:179853200-179857000	Weak transcription	Psoas Muscle	Psoas
14	chr1:179853200-179858800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:179853200-179858800	Weak transcription	Left Ventricle	heart
16	chr1:179853200-179859800	Weak transcription	Colonic Mucosa	Colon
17	chr1:179853200-179859800	Weak transcription	Gastric	stomach
18	chr1:179853200-179859800	Weak transcription	Pancreas	Pancrea
19	chr1:179853200-179861000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr1:179853200-179886600	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr1:179853200-179890800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr1:179853400-179858800	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr1:179853400-179859000	Weak transcription	HSMMtube	muscle
24	chr1:179853400-179859400	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr1:179853400-179872600	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr1:179853400-179877000	Weak transcription	Right Ventricle	heart
27	chr1:179853400-179878200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr1:179853400-179882800	Weak transcription	Fetal Brain Male	brain
29	chr1:179853600-179855600	Genic enhancers	Hela-S3	cervix
30	chr1:179853600-179855800	Genic enhancers	Brain Cingulate Gyrus	brain
31	chr1:179853600-179856200	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
32	chr1:179853600-179856200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
33	chr1:179853600-179858800	Weak transcription	Fetal Kidney	kidney
34	chr1:179853600-179859800	Weak transcription	Aorta	Aorta
35	chr1:179853600-179861600	Strong transcription	Placenta	Placenta
36	chr1:179853800-179855800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
37	chr1:179853800-179855800	Genic enhancers	Primary monocytes fromperipheralblood	blood
38	chr1:179853800-179855800	Strong transcription	Fetal Muscle Trunk	muscle
39	chr1:179853800-179855800	Strong transcription	Fetal Thymus	thymus
40	chr1:179853800-179855800	Strong transcription	NHDF-Ad	bronchial
41	chr1:179853800-179856000	Genic enhancers	Primary B cells from cord blood	blood
42	chr1:179853800-179856000	Genic enhancers	Liver	Liver
43	chr1:179853800-179856000	Genic enhancers	Duodenum Mucosa	Duodenum
44	chr1:179853800-179856000	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr1:179853800-179856000	Strong transcription	HMEC	breast
46	chr1:179853800-179856200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr1:179853800-179856200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr1:179853800-179856200	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
49	chr1:179853800-179856600	Genic enhancers	Primary neutrophils fromperipheralblood	blood
50	chr1:179853800-179857000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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