Variant report

Variant	rs417938
Chromosome Location	chr16:12082233-12082234
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:12070396..12074345-chr16:12081594..12084708,4	MCF-7	breast:
2	chr16:12077520..12080777-chr16:12082061..12084894,3	MCF-7	breast:
3	chr16:12069355..12070964-chr16:12081042..12083736,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260488	Chromatin interaction
ENSG00000234719	Chromatin interaction
ENSG00000048471	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11639821	0.91[MEX][hapmap]
rs378372	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs387027	0.86[AMR][1000 genomes]
rs393276	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs426424	1.00[CHB][hapmap]
rs436838	1.00[CHB][hapmap];0.85[JPT][hapmap];0.90[MEX][hapmap];0.93[YRI][hapmap];0.80[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs442234	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs446289	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6498261	0.86[MEX][hapmap]
rs7197059	0.95[MEX][hapmap]
rs8045634	0.82[MEX][hapmap]
rs86428	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042660	chr16:11846873-12110435	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv571458	chr16:11925008-12087282	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv905347	chr16:12010444-12243329	Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv1043096	chr16:12013915-12840769	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv482458	chr16:12014925-12145977	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	nsv1043959	chr16:12039346-12285269	Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs417938	TNFRSF17	cis	cerebellum	SCAN
rs417938	RP11-166B2.1	cis	Artery Tibial	GTEx
rs417938	TNFRSF17	cis	parietal	SCAN
rs417938	RP11-166B2.1	cis	Stomach	GTEx
rs417938	RP11-166B2.1	cis	Nerve Tibial	GTEx
rs417938	RP11-166B2.1	cis	Adipose Subcutaneous	GTEx
rs417938	GSPT1	cis	parietal	SCAN
rs417938	RP11-166B2.1	cis	Skin Sun Exposed Lower leg	GTEx
rs417938	RP11-166B2.1	cis	Esophagus Muscularis	GTEx
rs417938	RP11-166B2.1	cis	Whole Blood	GTEx

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12071400-12130800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr16:12071600-12083200	Weak transcription	Left Ventricle	heart
3	chr16:12071800-12083200	Weak transcription	Spleen	Spleen
4	chr16:12071800-12088200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr16:12071800-12140200	Weak transcription	Fetal Intestine Small	intestine
6	chr16:12072000-12086200	Weak transcription	Primary hematopoietic stem cells	blood
7	chr16:12072000-12087200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr16:12072000-12088200	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr16:12072000-12093600	Weak transcription	Fetal Stomach	stomach
10	chr16:12072200-12084600	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr16:12072200-12087400	Weak transcription	Fetal Thymus	thymus
12	chr16:12072200-12088200	Weak transcription	Duodenum Mucosa	Duodenum
13	chr16:12072200-12088200	Weak transcription	Right Ventricle	heart
14	chr16:12072200-12093800	Weak transcription	Thymus	Thymus
15	chr16:12072200-12096600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr16:12072200-12102600	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr16:12072400-12082400	Weak transcription	Placenta	Placenta
18	chr16:12072400-12083200	Weak transcription	Adipose Nuclei	Adipose
19	chr16:12072400-12086200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr16:12072400-12086200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr16:12072400-12087200	Weak transcription	Primary T cells from cord blood	blood
22	chr16:12072400-12096400	Weak transcription	Ovary	ovary
23	chr16:12072400-12104400	Weak transcription	NHLF	lung
24	chr16:12072600-12082400	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr16:12072600-12086200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr16:12072600-12094000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr16:12072600-12094000	Weak transcription	Stomach Smooth Muscle	stomach
28	chr16:12072600-12099000	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr16:12072800-12102800	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr16:12074600-12088200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr16:12076200-12083000	Weak transcription	GM12878-XiMat	blood
32	chr16:12076200-12083400	Weak transcription	Fetal Kidney	kidney
33	chr16:12078000-12082800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr16:12078800-12083200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr16:12079400-12083200	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr16:12079600-12085800	Weak transcription	Lung	lung
37	chr16:12079600-12109600	Weak transcription	Gastric	stomach
38	chr16:12080000-12083400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr16:12080200-12090000	Weak transcription	Aorta	Aorta
40	chr16:12080200-12093800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr16:12080400-12085000	Genic enhancers	Primary B cells from peripheral blood	blood
42	chr16:12080600-12082800	Weak transcription	Brain Angular Gyrus	brain
43	chr16:12080600-12088000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr16:12081000-12083200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr16:12082000-12091400	Enhancers	Primary monocytes fromperipheralblood	blood
46	chr16:12082000-12093000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr16:12082200-12083000	Enhancers	Brain Hippocampus Middle	brain
48	chr16:12082200-12083400	Genic enhancers	Primary B cells from cord blood	blood
49	chr16:12082200-12085200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr16:12082200-12086000	Enhancers	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links